Eukaryotic microorganisms for producing lipids and antioxidants

ABSTRACT

Disclosed are compositions and methods related to eukaryotic microorganisms that can produce unsaturated fatty acids which can be purified and used.

This application is a continuation application of U.S. patentapplication Ser. No. 13/427,562, filed Mar. 22, 2012, now U.S. Pat. No.8,921,069, which is a continuation application of, and claims benefit ofU.S. patent application Ser. No. 11/916,781, filed Jun. 23, 2008, nowU.S. Pat. No. 8,163,515, which is a national phase application of, andclaims benefit of PCT/IB2006/003977, filed Jun. 7, 2006, which claimsbenefit of and priority to U.S. Provisional Patent Application No.60/688,207, filed Jun. 7, 2005, and U.S. Provisional Application No.60/751,401, filed Dec. 16, 2005, all of which are incorporated byreference herein their entirety.

I. BACKGROUND

There is overwhelming scientific evidence that (n-3) highly unsaturatedfatty acids such as docosahexaenoic acid (DHA) have a positive effect oncardio-circulatory diseases, chronic inflammations and brain disorders.The (n-6) fatty acids on the other hand have been noted as intermediatemetabolites within the eicosanoid steroids, such as prostaglandins,leucotrienes or the like.

Currently, the main source of these highly unsaturated fatty acids isfish, with DHA and eicosapentaenoic acid (EPA) noted within various bluefish (such as sardines and tuna) at amounts around 20% and 10%,respectively. Yet, if one intends to use fish oil as the sole source ofthese lipids, several disadvantages exist, such as problems with flavortaint, uncontrollable fluctuations in availability, natural fish oilcontent variability, as well as the potential to accumulate harmfulenvironmental pollutants. In addition, if one intends to obtain a highlypurified (n-3) or (n-6) oil from these sources, it is very difficult topreferentially separate and purify.

II. SUMMARY

Disclosed are compositions and methods related to a eukaryote of theorder Thraustochytriales and family Thraustochytriaceae which whencultured produce quantities of unsaturated fatty acids, such as omega 3(n-3) and/or omega 6 (n-6) oils, such as DHA, EPA and DPA, capable ofbeing purified and used as all such compositions are used and more,because of their means of production

III. BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments and togetherwith the description illustrate the disclosed compositions and methods.

FIG. 1 shows a chart showing the results obtained from fatty acidmethylation of the lipids derived from ONC-T18.

FIG. 2 graphically depicts a fatty acid methyl ester comparison betweenthe original ONC-T18 isolate collected at Advocate Harbor and that ofthe ONC-T18 Thraustochytrium sp. deposited with ATCC as PTA-6245. Allpeaks were identified by Gas Chromatography and Mass Spectrometry.

FIG. 3 shows a scatter plot graph of results from ONC-T18 biomassoptimization experiments performed. These experiments used a techniqueknown as the Taguchi method in order to determine the optimal conditionsfor growth of ONC-T18 under various media conditions.

FIG. 4 shows a bar graph of the fatty acid profile of ONC-T18, grownunder optimal conditions (example 4) over a nine day period.

FIG. 5 shows a chart of oil producing organisms isolated as describedelsewhere herein.

FIG. 6 shows a branched phylogenetic tree of the relationship betweenthe 18S rRNA gene of ONC-T18 and other Thraustochytriales.

FIG. 7 shows lipid and DHA production of ONC-T18 under differentconditions.

FIG. 8 shows a modified graph with information about growth conditionson it for the eukaryotes disclosed herein. (Modified from Ratledge, C.(2004), Lipid Technol. 16:34-39).

FIG. 9 shows a proposed metabolic pathway for the production of PUFAsfor the disclosed eukaryotes.

FIG. 10 shows a comparison of fatty acid production maxima andcompositions under various alternative, low-cost carbon sources.

FIGS. 11A, 11B, 11C, and 11D, show a grouping of isolates collectedbased on their C20 and C22 PUFA profiles. Results were compared to tworeference strains: ATCC 20891 and MYA-1381.

FIG. 12 shows a 18S rRNA Neighbour joining tree of strain ONC-T18. Thebar represents genetic distance, while square brackets depict GenBankderived sequences used within this phylogenetic tree.

FIG. 13 shows the fatty acid profile of ONC-T18 grown in mediumcontaining 2 g L⁻¹ yeast extract, 8 g L⁻¹ L-glutamate, 6 g L⁻¹ sea saltand 60 g L⁻¹ glucose in 3 different types of fermentation: agar plate(1.5% agar, 25° C., 27 days), flasks (50 ml in 250 ml flask, 120 RPM,25° C., 3 days) and 5 L bioreactor (4 lpm air, pO₂ 90%, 25° C., 3 days).

FIG. 14 shows the HPLC chromatogram of carotenoid compounds isolatedfrom Thraustochytrium sp. ONC-T18. For example, Astaxanthin, Zeaxanthin,Canthaxanthin, Echinenone, and β-Carotene were isolated fromThraustochytrium sp. ONC-T18.

FIG. 15 shows typical biomass, total fatty acid (TFA), DHA productionand glucose utilization of Thraustochytrium sp. ONC-T18 maintained in a5 L bioreactor for 168 h with medium composed of 60 g L⁻¹ glucose, 2 gL⁻¹ yeast extract, 8 g L⁻¹ glutamic acid and 6 g L⁻¹ salt (4 lpm air,pO₂ 90%, 25° C., pH 7-9).

FIG. 16 shows postulated pathways involved in the formation ofastaxanthin in Thraustochytrium sp. ONC-T18.

IV. DETAILED DESCRIPTION

Before the present compounds, compositions, articles, devices, and/ormethods are disclosed and described, it is to be understood that theyare not limited to specific synthetic methods or specific recombinantbiotechnology methods unless otherwise specified, or to particularreagents unless otherwise specified, as such may, of course, vary. It isalso to be understood that the terminology used herein is for thepurpose of describing particular embodiments only and is not intended tobe limiting.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the method and compositions described herein. Suchequivalents are intended to be encompassed by the claims below.

A. DEFINITIONS

As used in the specification and the appended claims, the singular forms“a,” “an” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a pharmaceuticalcarrier” includes mixtures of two or more such carriers, and the like.

Ranges can be expressed herein as from “about” one particular value,and/or to “about” another particular value. When such a range isexpressed, another embodiment includes from the one particular valueand/or to the other particular value. Similarly, when values areexpressed as approximations, by use of the antecedent “about,” it willbe understood that the particular value forms another embodiment. Itwill be further understood that the endpoints of each of the ranges aresignificant both in relation to the other endpoint, and independently ofthe other endpoint. It is also understood that there are a number ofvalues disclosed herein, and that each value is also herein disclosed as“about” that particular value in addition to the value itself. Forexample, if the value “10” is disclosed, then “about 10” is alsodisclosed. It is also understood that when a value is disclosed that“less than or equal to” the value, “greater than or equal to the value”and possible ranges between values are also disclosed, as appropriatelyunderstood by the skilled artisan. For example, if the value “10” isdisclosed then “less than or equal to 10” as well as “greater than orequal to 10” is also disclosed. It is also understood that throughoutthe application, data is provided in a number of different formats, andthat this data, represents endpoints and starting points, and ranges forany combination of the data points. For example, if a particular datapoint “10” and a particular data point “15” are disclosed, it isunderstood that greater than, greater than or equal to, less than, lessthan or equal to, and equal to 10 and 15 are considered disclosed aswell as between 10 and 15. It is also understood that each unit betweentwo particular units are also disclosed. For example, if 10 and 15 aredisclosed, then 11, 12, 13, and 14 are also disclosed.

By “reduce” or other forms of reduce means lowering of an event orcharacteristic. It is understood that this is typically in relation tosome standard or expected value, in other words it is relative, but thatit is not always necessary for the standard or relative value to bereferred to. For example, “reduces phosphorylation” means lowering theamount of phosphorylation that takes place relative to a standard or acontrol. It is understood that unless specifically indicated otherwise,a compound or composition or condition can be reduced relative toanother compound or composition or condition.

By “inhibit” or other forms of inhibit means to hinder or restrain aparticular characteristic. It is understood that this is typically inrelation to some standard or expected value, in other words it isrelative, but that it is not always necessary for the standard orrelative value to be referred to. For example, “inhibitsphosphorylation” means hindering or restraining the amount ofphosphorylation that takes place relative to a standard or a control. Itis understood that unless specifically indicated otherwise, a compoundor composition or condition can be inhibited relative to anothercompound or composition or condition.

By “prevent” or other forms of prevent means to stop a particularcharacteristic or condition. Prevent does not require comparison to acontrol as it is typically more absolute than, for example, reduce orinhibit. As used herein, something could be reduced but not inhibited orprevented, but something that is reduced could also be inhibited orprevented. It is understood that where reduce, inhibit or prevent areused, unless specifically indicated otherwise, the use of the other twowords is also expressly disclosed. Thus, if inhibits phosphorylation isdisclosed, then reduces and prevents phosphorylation are also disclosed.

The term “therapeutically effective” means that the amount of thecomposition used is of sufficient quantity to ameliorate one or morecauses or symptoms of a disease or disorder. Such amelioration onlyrequires a reduction or alteration, not necessarily elimination.

The term “carrier” means a compound, composition, substance, orstructure that, when in combination with a compound or composition, aidsor facilitates preparation, storage, administration, delivery,effectiveness, selectivity, or any other feature of the compound orcomposition for its intended use or purpose. For example, a carrier canbe selected to minimize any degradation of the active ingredient and tominimize any adverse side effects in the subject.

Throughout the description and claims of this specification, the word“comprise” and variations of the word, such as “comprising” and“comprises,” means “including but not limited to,” and is not intendedto exclude, for example, other additives, components, integers or steps.

The term “cell” as used herein also refers to individual microbialcells, or cultures derived from such cells. A “culture” refers to acomposition comprising isolated cells of the same or a different type.

The term “metabolite” refers to active derivatives produced uponintroduction of a compound into a biological milieu, such as a patient.

When used with respect to pharmaceutical and nutraceutical compositions,the term “stable” is generally understood in the art as meaning lessthan a certain amount, usually 10%, loss of the active ingredient underspecified storage conditions for a stated period of time. The timerequired for a composition to be considered stable is relative to theuse of each product and is dictated by the commercial practicalities ofproducing the product, holding it for quality control and inspection,shipping it to a wholesaler or direct to a customer where it is heldagain in storage before its eventual use. Including a safety factor of afew months time, the minimum product life for pharmaceuticals is usuallyone year, and preferably more than 18 months. As used herein, the term“stable” references these market realities and the ability to store andtransport the product at readily attainable environmental conditionssuch as refrigerated conditions, 2° C. to 8° C.

References in the specification and concluding claims to parts byweight, of a particular element or component in a composition orarticle, denotes the weight relationship between the element orcomponent and any other elements or components in the composition orarticle for which a part by weight is expressed. Thus, in a compoundcontaining 2 parts by weight of component X and 5 parts by weightcomponent Y, X and Y are present at a weight ratio of 2:5, and arepresent in such ratio regardless of whether additional components arecontained in the compound.

A weight percent of a component, unless specifically stated to thecontrary, is based on the total weight of the formulation or compositionin which the component is included.

“Isolating” and any form such as “isolate” refer to a situation wheresomething is in a form wherein it can be manipulated or furtherpurified. Isolated and its forms indicates that something is in acurrent state which is different than a previous state. For example, aribosomal RNA molecule can be “isolated” if it is, for example removedfrom an organism, synthesized or recombinantly produced. Often, the“isolation” of one thing is in relation to something else. For example,a eukaryote as discussed herein can be isolated as discussed herein, by,for example, culturing the eukaryote, such that the eukaryote survivesin the absence of appreciable amounts (detectable) of other organisms.It is understood that unless specifically indicated otherwise, any ofthe disclosed compositions can be isolated as disclosed herein.

“Purify” and any form such as “purifying” refers to the state in which asubstance or compound or composition is in a state of greaterhomogeneity than it was before. It is understood that as disclosedherein, something can be, unless otherwise indicated, at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, or 100% pure. For example, if given composition Awas 90% pure, this would mean that 90% of the composition was A, andthat 10% of the composition was one or more things, such as molecules,compounds, or other substances. For example, if a disclosed eukaryoticmicroorganism, for example, produces 35% DHA, this could be further“purified” such that the final lipid composition was greater than 90%DHA. Unless otherwise indicated, purity will be determined by therelative “weights” of the components within the composition. It isunderstood that unless specifically indicated otherwise, any of thedisclosed compositions can be purified as disclosed herein.

“Optional” or “optionally” means that the subsequently described eventor circumstance may or may not occur, and that the description includesinstances where said event or circumstance occurs and instances where itdoes not.

“Primers” are a subset of probes which are capable of supporting sometype of enzymatic manipulation and which can hybridize with a targetnucleic acid such that the enzymatic manipulation can occur. A primercan be made from any combination of nucleotides or nucleotidederivatives or analogs available in the art which do not interfere withthe enzymatic manipulation.

Throughout this application, various publications are referenced. Thedisclosures of these publications in their entireties are herebyincorporated by reference into this application in order to more fullydescribe the state of the art to which this pertains. The referencesdisclosed are also individually and specifically incorporated byreference herein for the material contained in them that is discussed inthe sentence in which the reference is relied upon.

Disclosed are the components to be used to prepare the disclosedcompositions as well as the compositions themselves to be used withinthe methods disclosed herein. These and other materials are disclosedherein, and it is understood that when combinations, subsets,interactions, groups, etc. of these materials are disclosed that whilespecific reference of each various individual and collectivecombinations and permutation of these compounds may not be explicitlydisclosed, each is specifically contemplated and described herein. Forexample, if a particular species of the family Thraustochytriaceae isdisclosed and discussed and a number of modifications that can be madeto a number of organisms including species of the familyThraustochytriaceae are discussed, specifically contemplated is each andevery combination and 10 permutation of these species from the familyThraustochytriaceae and the modifications that are possible unlessspecifically indicated to the contrary. Thus, if a class of molecules A,B, and C are disclosed as well as a class of molecules D, E, and F andan example of a combination molecule, A-D is disclosed, then even ifeach is not individually recited each is individually and collectivelycontemplated meaning combinations, A-E, A-F, B-D, B-E, B-F, C-D, C-E,and C-F are considered disclosed. Likewise, any subset or combination ofthese is also disclosed. Thus, for example, the sub-group of A-E, B-F,and C-E would be considered disclosed. This concept applies to allaspects of this application including, but not limited to, steps inmethods of making and using the disclosed compositions. Thus, if thereare a variety of additional steps that can be performed it is understoodthat each of these additional steps can be performed with any specificembodiment or combination of embodiments of the disclosed methods.

B. COMPOSITIONS

Disclosed are eukaryotic microorganisms of the order Thraustochytriales,preferably Thraustochytrium or Schizochytrium species, having theability to produce lipids, such as fatty acids, such as unsaturatedfatty acids, such as omega-3 fatty acids, such as omega-6 fatty acids,and omega-9 fatty acids, such as the (n-3) series of docosahexaenoicacid (DHA) and eicosapentaenoic acid (EPA), (n-6) series ofdocosapentaenoic acid (DPA) and the (n-9) series of palmitic and stearicacids. The disclosed eukaryotic microorganisms can also produceantioxidants, such as but not limited to the carotenoid compoundcarotene, (for example β-carotene) and the xanthophylls compoundsastaxanthin, zeaxanthin, canthaxanin, and echinenone.

Also disclosed are conditions for the isolation and growth of theeukaryotic microorganisms. For example, herewith are heterotrophicgrowth conditions for production of the disclosed lipids andantioxidants, for example, both individually and cumulatively.Accordingly, it is possible through the use of this unique eukaryote, toeffectively produce the (n-3) series of DHA and/or the (n-6) series ofDPA and/or the carotenoid series of antioxidant compounds and/or thexanthophylls series of antioxidant compounds, which are useful as orwithin nutraceuticals, food additives, pharmaceuticals or industry.

Disclosed are compositions comprising a eukaryotic microorganismcomprising or consisting of a Thraustochytrium species, an example asdisclosed herein being the ONC-T18 strain which has a deposit number ofATCC accession number PTA-6245.

It is understood that the eukaryotic microorganism and any clones,modified organisms or genes isolated from said organism as set forth inONC-T18 are also disclosed. The disclosed organisms have the ability toproduce unsaturated fatty acids, such as lipids containing the omega-3series of DHA and EPA, and the omega-6 series of DPA and variousantioxidant such as carotenoids, xanthophylls and phenolics.

Also disclosed are processes for the production of biomass containingsaid compounds. Further disclosed are processes for preparing omega-3,omega-6 and carotenoid compounds utilizing the eukaryotic microorganism.Also disclosed are processes for the production of microbial derived (orsingle celled) oils.

In addition, disclosed are the fatty acids and carotenoids produced bythe disclosed eukaryotic microorganism and any progeny (geneticallymodified or otherwise), various feedstuffs, nutraceuticals,pharmaceutical and food supplemented with the lipids and antioxidants,as well as a process for utilizing these compounds as an additive forvarious feedstuffs and foods.

U.S. Pat. No. 5,130,242 to Barclay disclosed a collection and screeningprocess to isolate strains of microorganisms with the followingcharacteristics for the production of omega-3 fatty acids: 1) capable ofheterotrophic growth; 2) produce a high content of omega-3 fatty acids;3) unicellular; 4) produce a low content of standard and omega-6 fattyacids; 5) non-pigmented, white or colorless cells; 6) thermotolerant(e.g., ability to grow above 30° C.); and 7) eurhaline (e.g., ability togrow at a wide range of salinities, but preferably at low salinity).

The '242 disclosure also describes a process for the heterotrophicproduction of whole-celled or extracted microbial products with a highconcentration of omega-3 fatty acids, which can later be used in animalor human food products. This process uses microorganisms identified bythe collection and screening process disclosed thereof. Thesemicroorganism, which are of the order Thaustochytriales, are cultured inground grain. To enhance production of omega-3 fatty acids, lowtemperature stressing and high dissolved oxygen are used, as well as theaddition of antioxidants, growth factors, vitamins, and phosphorous. Theextracted products contain high concentrations of omega-3 fatty acids(e.g., C20:5w3, C22:5w3; and C22:6w3) and low concentrations of omega-6fatty acids (e.g., C20:4w6 and C22:5w6). Specifically, the ratios of theC20:5w3 to C22:6w3 fatty acids run from 1:1 to 1:30. Ratios of C22:5w3to C22:6w3 fatty acids run from 1:12 to only trace amounts of C22:5w3.Also, the microorganisms produce from 0.6 to 0.72% DHA, 0 to 5% DPA, and0 to 18.9% EPA, by weight of total fatty acid.

U.S. Pat. No. 6,451,567 to Barclay disclosed a process for growingThraustochytrium and Schizochytrium in a non-chloride medium (<3 g/L)containing sodium salts (e.g., sodium sulfate). The non-chloride mediumresults in cell aggregate sizes of less than 150 μm. The disclosedprocess produces microorganisms and extracts that are useful in foodproducts for aquaculture. Further components of the food productsinclude flaxseed, rapeseed, soybean, and avocado meal. Themicroorganisms can produce 1.08 g/L of medium per day of omega-3 fattyacids. The '567 disclosure further describes various culture mediums,which include sea water, glucose (1, 3, 5, or 10 g/L), yeast extract(0.01, 0.2, 0.4 and 5 g/L), additional nitrogen sources such as proteinhydrosylate (1 g/L), liver extract (1 g/L), glutamate (5 g/L), MSG (3g/L), and additional salts, trace vitamins and minerals (e.g., KH₂PO₄,MgSO₄, and gelatin extract).

U.S. Pat. No. 6,582,941 to Yokochi et al. discloses a Schizochytriumspecies, strain SR21 and another Schizochytrium strain belonging to thesame species that have the ability to produce fatty acid fractionshaving a high concentration of omega-3 DHA and/or omega-6 DPA and a lowconcentration of EPA. Also, disclosed are methods of culturing suchmicroorganisms and isolating such fatty acids. The medium used containssea salt, yeast extract (0.2, 1.0, or 10 g/L), corn steep liquor (0.5,1.0, or 10 g/L), glucose (10-120 g/L), plus additional salts (e.g.,NH₄OAc, phosphates). The fatty acid compositions contain about 15 to 20%DHA by weight of biomass (about 28% by weight of total fatty acid). Thecompositions can be used in food products (e.g., baby milk).

U.S. Pat. No. 6,607,900 to Bailey et al. disclosed a process for growingeukaryotic microorganisms (e.g., Schizochytrium sp. ATCC No. 20888) thatare capable of producing at least 20% of their biomass aspolyunsaturated lipids (particularly omega-3 and -6 fatty acids). Theprocess involves culturing the microorganisms in a medium containing acarbon and nitrogen source. Also disclosed is the use of low dissolvedoxygen levels (less than 3%) and low chloride ion levels (less than 3g/L) to enhance production. The microorganisms have a lipid productionrate of at least 0.5 g/L/h. The lipid fraction is from 15 to 20% DHA byweight of biomass (about 35% by weight of total fatty acid methylester).

U.S. Publication No. 2004/0161831 to Komazawa et al discloses aThraustochytrium strain (LEFT; ATCC No. FERM BP-08568) that has theability to produce DHA. By culturing in conventional media, themicroorganism can produce oil with at least 50% by weight DHA. The oilcan be treated with a lipase prior to isolation of DHA. The oil can beused in food or drinks or the DHA can be hydrolyzed to produce behenicacid.

1. Fatty Acids

Fatty acids are hydrocarbon chains that terminate in a carboxyl group,being termed unsaturated if they contain at least one carbon-carbondouble bond, and polyunsaturated when they contain multiple such bonds.Long-chain polyunsaturated fatty acids (PUFA) or highly-unsaturatedfatty acids (HUFA), may be divided into the (n-3) and (n-6) series as aresult of the location of these double bonds. There is overwhelmingscientific evidence that (n-3) highly unsaturated fatty acids such asDHA have a positive effect on cardio-circulatory diseases, chronicinflammation and brain disorders. The (n-6) fatty acids on the otherhand have been noted as intermediate metabolites within the eicosanoidsteroids, such as prostaglandins, leucotrienes or the like.

Polyunsaturated fatty acids can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or10 double and/or triple carbon-carbon bonds. For example,polyunsaturated fatty acids can comprise 3-8, 4-7, or 5-6 double and/ortriple carbon-carbon bonds.

Currently, the main source of these highly unsaturated fatty acids isfish, with DHA and EPA noted within various blue fish (such as sardinesand tuna) at amounts around 20% and 10%, respectively. Yet, if oneintends to use fish oil as the sole source of these lipids, severaldisadvantages exist, such as problems with flavor taint, uncontrollablefluctuations in availability, natural fish oil content variability, aswell as the potential to accumulate harmful environmental pollutants. Inaddition, if one intends to obtain a highly purified (n-3) or (n-6) oilfrom said sources, it is very difficult to preferentially separate andpurify. Specifically, a large market is available within the neonatalsupplement market for a highly concentrated form of DHA. If fish oilwere to be the source of said products, then DHA would have to bepreferentially isolated in large quantities from EPA. Clearly analternative source of highly purified and production tailored source ofthese highly unsaturated fatty acids is needed.

In addition to fish oils, various microorganisms (mainly marine) areable to produce and/or accumulate the (n-3) series of docosahexaenoicacid. Of particular interest is the fact that microbial production isnot subject to fluctuations caused by external variables such asseasonality, weather and food supply. For example, the followingmicroorganisms are known as having the ability to produce DHA: thedeep-sea derived bacterium Vibrio marinus (ATCC 15381), Vibrio sp.T3615, Photobacterium profundum SS9, Mortierella marina MP-1 andPsychromonas kaikoae (ATCC BAA-363T); microalgal species such asCrypthecodinium cohnii, Cyclotella cryptica, and Mortieralla alpina(1S-4); and the protists Thraustochytrium sp. (ATCC 20892),Thraustochytrium aureum (ATCC 34304) and Thraustochytrium roseum.According to a process utilizing these purified organisms, however, theamount of docosahexaenoic acid produced per gram of biomass per liter islow, being within the range of 10 to 500 mg. Some examples andrepresentative microbial oil producing organisms are shown in FIG. 5.

Omega 3s have been shown to have beneficial effects and the oils andcompositions disclosed herein can be used for anti-inflammatory effecton cystic fibrosis (Cochrane Database Syst Rev. 3), rheumatoid arthritis(Drugs 63: 845-53), asthma (Ann Allergy Asthma Immunol 90: 371-7) andthrombotic stroke (Prev Cardiol 6: 38-1), cardio-protective, as well asa direct effect on artheriosclerosis and arrhythmia (ProstaglandinsLeukot Essent Fatty Acids. 63:351-62), inhibition of cancerproliferation in breast and prostate cancer cell lines and reduction inanimal experiments (Am J Clin Nutr 77: 532-43), anti-psychotic effect onschizophrenia (J Neural Transm Suppl 64:105-17) and other psychiatricdiseases (Can J Psychiatry 48: 195-203), immunonutrient supplement usedfor normal neonatal development and in the treatment of neonatalinfections (Eur J Pediatr 162: 122-8), and pathological pain treatmentby directly attenuate the neuronal and ganglial processes that underlieneuropathic and inflammatory pain (Prostaglandins Leukot Essent FattyAcids 68: 219-24).

2. Thraustochytriaceae

a) ONC-T18

The marine organism ONC-T18, as disclosed herein, was collected as partof a PUFA producing microbial isolation trip, with over 60 pure culturesisolated (see table 7 for details). Further, ONC-T18 was isolated fromthe leaves of salt marsh grasses in the Advocate Harbor, Bay of Fundy,Nova Scotia, Canada. Through microscopic examinations and serial culturepurification techniques, the strain was believed to be a singlemicroorganism belonging to the genus Thraustochytrium. All strains andtwo ATCC comparison cultures (ATCC 20891 & MYA-1381) were grown on 0.5%glucose, 0.2% peptone, 0.2% yeast extract in sea-water (SW) andunderwent GC (fatty acid methyl ester, FAME) analysis.

FIG. 6 shows a proposed phylogenetic tree of the relationship betweenONC-T18, and other closely related organisms.

ONC-T18 was originally isolated as a single microbe using classic pinepollen baiting techniques, followed by culturing on selective medium.Specifically, a nutrient medium containing 5 g L⁻¹ glucose, 2 g L⁻¹peptone, 2 g L⁻¹ yeast extract to 1 L of 0.2 μm filtered sea water wasprepared. The fatty acid profile of ONC-T18 was then determined usingthe Bligh and Dyer extraction method and PUFA gas chromatographictechniques. Chromatographic results demonstrated the ability of thisstrain to produce increased amounts of TFA, DHA, as well as markedquantities of EPA and DPA.

The disclosed eukaryotic microorganism can be used in a process forpreparing a lipid or fat containing DHA, EPA and DPA, but is not limitedto the above-mentioned ONC-T18 or PTA-6245 strain, but any derivation ofsaid strain whether it be via genetic modification, chemicalmutagenesis, fermentative adaptation or any other means of producingmutants of the strain, whereby the product of these modifications havegenetic or morphological and functional features such as the eukaryoticmicroorganism, as disclosed herein.

Disclosed are eukaryotic microorganism capable of producing a lipidcomposition having distinctive lipid class properties, and the solutionto the problem of maintaining a stable, reliable and economical sourcefor such a lipid having high functionality and additional valueaccording to the same. Therefore, wild-type strains producing the (n-3)series of DHA and the (n-6) series of DPA to a greater degree as well asvariant and recombinant strains designed to produce thesepolyunsaturated fatty acids to a greater degree are disclosed herein.Such variant or recombinant microorganisms include those designed tohave a higher content of said lipids than those produced by the originalwild-type strain, when cultured using the same conditions and media. Inaddition, microorganisms designed to produce a lipid containing similaramounts of the (n-3) series of DHA, EPA and the (n-6) series of DPA canbe selected, as compared with the corresponding wild-type strains,effectively using substrates having a superior cost performance, arealso included.

Disclosed are compositions comprising a eukaryotic microorganism of theorder Thraustochytriales wherein the eukaryotic microorganism producesunsaturated fatty acids. The polyunsaturated fatty acids can be, forexample, omega 3 or omega 6 fatty acids, such as DHA and DPA.

Disclosed are compositions comprising a eukaryote, wherein thecomposition produces a lipid.

Also disclosed are compositions wherein the lipid comprises a lipid asdisclosed herein.

Also disclosed are compositions, wherein the eukaryote comprises amember of the order Thraustochytriales.

Also disclosed are compositions, wherein the eukaryote has a 18Sribosome RNA gene sequence having at least 80% identity to SEQ ID NO:1.

It is understood that any form of characterization described herein,such as by genetics or by the lipid signatures or by theclassifications, for the eukaryotic microorganisms can be used tocharacterize the microorganisms as disclosed herein. The eukaryoticmicroorganism can comprise one or more microorganisms from the familyThraustochytriaceae, and examples are ATCC accession number 20888,20889, 20890, 20891, and 20892. There are a variety of characteristicsthat can be used related to the organisms and the unsaturated fattyacids they produce. It is understood that these can be used in anycombination or permutation to define a set or sets of organisms or oilsor antioxidants, for example. One characteristic is the classificationof the organisms themselves, the genetic identification of theorganisms, the lipid and antioxidant profiles of the organisms, and thegrowth conditions of the organisms, for example.

b) Classification

The eukaryotic microorganism can be from the phylum Labyrinthulomycota.The eukaryotic microorganism can be from the class Labyrinthulomycetes.The eukaryotic microorganism can be from the subclass Thraustochytridae.The eukaryotic microorganism can be from the order Thraustochytriales.The eukaryotic microorganism can be from the family Thraustochytriaceae.The eukaryotic microorganism can be from the genus Thraustochytrium. Theeukaryotic microorganism can be a Thraustochytrium sp. The eukaryoticmicroorganism can be Thraustochytrium aureum. The eukaryoticmicroorganism can be Thraustochytrium roseum. The eukaryoticmicroorganism can be Thraustochytrium striatum. The eukaryoticmicroorganism can be from the genus Schizochytrium. The eukaryoticmicroorganism can be Schizochytrium sp. The eukaryotic microorganism canbe a modified version of any of the listed eukaryotic microorganisms.The eukaryotic microorganism can also comprise any currently unknown orisolated members of said prokaryotes class, subclass, order, family orgenus. A combination of eukaryotic microorganisms can be any combinationof any organisms disclosed herein, including, one or more of theThraustochytrium sp., Schizochytrium sp., Thraustochytrium aureum,Thraustochytrium striatum and Thraustochytrium roseum.

The eukaryotic microorganisms from the family Thraustochytriaceae can beany of those disclosed above. The eukaryotic microorganism can comprisethe organism having ATCC accession number PTA-6245.

c) Genetics

The eukaryotic microorganism can have 18S rRNA sequence SEQ ID NO:1. Theeukaryotic microorganism can have an 18S rRNA sequence that, forexample, has about 90% homology, or any other identity disclosed herein,to SEQ ID NO:1. The eukaryotic microorganism can have an 18S rRNAsequence that hybridizes under stringent conditions, or any otherconditions as disclosed herein, to SEQ ID NO:1, or a portion of SEQ IDNO:1.

The sequence similarity/identity and nucleic acid hybridization of thenucleic acids of the organisms can be as described herein. Specifically,comparison of SEQ ID NO:1 with nucleic acid sequences found in thegenomic database, GenBank (National Centre for BiotechnologyInformation, National Institute of Health, Bethesda, Md., USA) using theBLAST (Basic local alignment search tool) algorithm identified SEQ IDNO:1 as being related (91% similarity) to several eukaryoticThraustochytrid species, closely related to Thraustochytrium sp. CHN-1[AB126669] (94.5% similarity) and Thraustochytriidae sp. N1-27[AB073308] (95.5% similarity), and most closely related toThraustochytrium striatum [AF265338] (97.5% similarity).

3. (1) Sequence Similarities

It is understood that as discussed herein the use of the terms homologyand identity mean the same thing as similarity. Thus, for example, ifthe use of the word homology is used between two non-natural sequencesit is understood that this is not necessarily indicating an evolutionaryrelationship between these two sequences, but rather is looking at thesimilarity or relatedness between their nucleic acid sequences. Many ofthe methods for determining homology between two evolutionarily relatedmolecules are routinely applied to any two or more nucleic acids orproteins for the purpose of measuring sequence similarity regardless ofwhether they are evolutionarily related or not.

In general, it is understood that one way to define any known variantsand derivatives or those that might arise, of the disclosed genes andproteins herein, is through defining the variants and derivatives interms of homology to specific known sequences. This identity ofparticular sequences disclosed herein is also discussed elsewhereherein. In general, variants of nucleic acids and proteins hereindisclosed typically have at least, about 50, 55, 60, 65, 70, 71, 72, 73,74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the statedsequence or the native sequence. Those of skill in the art readilyunderstand how to determine the homology of two proteins or nucleicacids, such as genes. For example, the homology can be calculated afteraligning the two sequences so that the homology is at its highest level.

Another way of calculating homology can be performed by publishedalgorithms. Optimal alignment of sequences for comparison may beconducted by the local homology algorithm of Smith and Waterman Adv.Appl. Math. 2:482, 1981, by the homology alignment algorithm ofNeedleman and Wunsch, J. Mol. Biol. 48:443, 1970, by the search forsimilarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA85:2444, 1988, by computerized implementations of these algorithms (GAP,BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group, 575 Science Dr., Madison, Wis.), or byinspection.

The same types of homology can be obtained for nucleic acids by forexample the algorithms disclosed in Zuker, M. Science 244:48-52, 1989,Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger etal. Methods Enzymol. 183:281-306, 1989 which are herein incorporated byreference for at least material related to nucleic acid alignment. It isunderstood that any of the methods typically can be used and that incertain instances the results of these various methods may differ, butthe skilled artisan understands if identity is found with at least oneof these methods, the sequences would be said to have the statedidentity, and be disclosed herein.

For example, as used herein, a sequence recited as having a particularpercent homology to another sequence refers to sequences that have therecited homology as calculated by any one or more of the calculationmethods described above. For example, a first sequence has 80 percenthomology, as defined herein, to a second sequence if the first sequenceis calculated to have 80 percent homology to the second sequence usingthe Zuker calculation method even if the first sequence does not have 80percent homology to the second sequence as calculated by any of theother calculation methods. As another example, a first sequence has 80percent homology, as defined herein, to a second sequence if the firstsequence is calculated to have 80 percent homology to the secondsequence using both the Zuker calculation method and the Pearson andLipman calculation method even if the first sequence does not have 80percent homology to the second sequence as calculated by the Smith andWaterman calculation method, the Needleman and Wunsch calculationmethod, the Jaeger calculation methods, or any of the other calculationmethods. As yet another example, a first sequence has 80 percenthomology, as defined herein, to a second sequence if the first sequenceis calculated to have 80 percent homology to the second sequence usingeach of calculation methods (although, in practice, the differentcalculation methods will often result in different calculated homologypercentages).

(2) Hybridization/Selective Hybridization

The term hybridization typically means a sequence driven interactionbetween at least two nucleic acid molecules, such as a primer or a probeand a gene. Sequence driven interaction means an interaction that occursbetween two nucleotides or nucleotide analogs or nucleotide derivativesin a nucleotide specific manner. For example, G interacting with C or Ainteracting with T are sequence driven interactions. Typically sequencedriven interactions occur on the Watson-Crick face or Hoogsteen face ofthe nucleotide. The hybridization of two nucleic acids is affected by anumber of conditions and parameters known to those of skill in the art.For example, the salt concentrations, pH, and temperature of thereaction all affect whether two nucleic acid molecules will hybridize.

Parameters for selective hybridization between two nucleic acidmolecules are well known to those of skill in the art. For example, insome embodiments selective hybridization conditions can be defined asstringent hybridization conditions. For example, stringency ofhybridization is controlled by both temperature and salt concentrationof either or both of the hybridization and washing steps. For example,the conditions of hybridization to achieve selective hybridization mayinvolve hybridization in high ionic strength solution (6×SSC or 6×SSPE)at a temperature that is about 12-25° C. below the T_(m) (the meltingtemperature at which half of the molecules dissociate from theirhybridization partners) followed by washing at a combination oftemperature and salt concentration chosen so that the washingtemperature is about 5-20° C. below the T_(m). The temperature and saltconditions are readily determined empirically in preliminary experimentsin which samples of reference DNA immobilized on filters are hybridizedto a labeled nucleic acid of interest and then washed under conditionsof different stringencies. Hybridization temperatures are typicallyhigher for DNA-RNA and RNA-RNA hybridizations. The conditions can beused as described above to achieve stringency, or as is known in theart. (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed.,Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989; Kunkel etal. Methods Enzymol. 154:367, 1987 which is herein incorporated byreference for material at least related to hybridization of nucleicacids). A preferable stringent hybridization condition for a DNA:DNAhybridization can be at about 68° C. (in aqueous solution) in 6×SSC or6×SSPE followed by washing at 68° C. Stringency of hybridization andwashing, if desired, can be reduced accordingly as the degree ofcomplementarity desired is decreased, and further, depending upon theG-C or A-T richness of any area wherein variability is searched for.Likewise, stringency of hybridization and washing, if desired, can beincreased accordingly as homology desired is increased, and further,depending upon the G-C or A-T richness of any area wherein high homologyis desired, all as known in the art.

Another way to define selective hybridization is by looking at theamount (percentage) of one of the nucleic acids bound to the othernucleic acid. For example, in some embodiments selective hybridizationconditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75,76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100 percent of the limiting nucleic acid isbound to the non-limiting nucleic acid. Typically, the non-limitingprimer is in for example, 10 or 100 or 1000 fold excess. This type ofassay can be performed under conditions where both the limiting andnon-limiting primer are for example, 10, 100 or 1000 fold below theirk_(d), or where only one of the nucleic acid molecules is 10, 100 or1000 fold or where one or both nucleic acid molecules are above theirk_(d).

Another way to define selective hybridization is by looking at thepercentage of primer that gets enzymatically manipulated underconditions where hybridization is required to promote the desiredenzymatic manipulation. For example, in some embodiments selectivehybridization conditions would be when at least about, 50, 55, 60, 65,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 10 percent of theprimer is enzymatically manipulated under conditions which promote theenzymatic manipulation, for example if the enzymatic manipulation is DNAextension, then selective hybridization conditions would be when atleast about 50, 55, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,99, 100 percent of the primer molecules are extended. Preferredconditions also include those suggested by the manufacturer or indicatedin the art as being appropriate for the enzyme performing themanipulation.

Just as with homology, it is understood that there are a variety ofmethods herein disclosed for determining the level of hybridizationbetween two nucleic acid molecules. It is understood that these methodsand conditions may provide different percentages of hybridizationbetween two nucleic acid molecules, but unless otherwise indicatedmeeting the parameters of any of the methods would be sufficient. Forexample, if 80% hybridization was required and as long as hybridizationoccurs within the required parameters in any one of these methods it isconsidered disclosed herein.

It is understood that those of skill in the art understand that if acomposition or method meets any one of these criteria for determininghybridization either collectively or singly it is a composition ormethod that is disclosed herein.

b) Composition of Molecules Produced

It is understood that the eukaryotes disclosed herein are capable ofproducing a number of compounds and compositions. The compounds andcompositions can be used as a signature, a way of identifying theorganism. For example, one way of characterizing an organism is by thelipid profile that the organism produces. As disclosed herein thesevarious lipid profiles can be used to characterize the organism as wellas be purified, manipulated, and collected for a variety of reasons.

(1) Lipids

It is understood that each organism can produce some profile ofunsaturated fatty acids, as disclosed herein. These profiles arecharacteristics of the organisms. Below are some examples, ofunsaturated and other lipid profiles for the organisms.

The eukaryotic microorganism can produce, for example a lipid or fattyacid fraction of at least about 4 wt. % to 6 wt. % (e.g., about 5 wt.%), which comprises from about 0 wt. % to about 2 wt. % myristic acid(e.g., about 1 wt. %), from about 16 wt. % to about 20 wt. % (e.g.,about 18 wt. %) palmitic acid, from about 0 wt. % to about 2 wt. %(e.g., about 1 wt. %) palmitoleic acid, from about 4 wt. % to about 8wt. % (e.g., about 6 wt. %) stearic acid, from about 30 wt. % to about34 wt. % (e.g., about 32 wt. %) oleic acid, from about 40 wt. % to about44 wt. % (e.g., about 42 wt. %) linoleic acid, and from about 0 wt. % toabout 3 wt. % (e.g., about 2 wt. %) n-3 EPA per dried cellular biomass.

The eukaryotic microorganism can also produce, for example, a lipid orfatty acid fraction of at least about 1 wt. % to 3 wt. % (e.g., about1.25 wt. %), which comprises from about 2 wt. % to about 4 wt. % (e.g.,about 3 wt. %) myristic acid, from about 50 wt. % to about 60 wt. %(e.g., about 55 wt. %) palmitic acid, from about 2 wt. % to about 4 wt.% (e.g., about 3 wt. %) palmitoleic acid, from about 16 wt. % to about20 wt. % (e.g., about 18 wt. %) stearic acid, from about 9 wt. % toabout 13 wt. % (e.g., about 11 wt. %) oleic acid, from about 1 wt. % toabout 3 wt. % (e.g., about 2 wt. %) eicosadienoic acid, and from about 6wt. % to about 10 wt. % (e.g., about 8 wt. %) n-3 EPA per dried cellularbiomass.

The eukaryotic microorganism, for example, such as ONC-T18, can produceat least about 30 wt. %, 40 wt. %, 50 wt. %, 60 wt. %, 70% wt. % or 80wt. % (e.g., about 80 wt. %) of a lipid composition per dried cellularbiomass. For example, the eukaryotic microorganism can produce a lipidcomposition comprising from about 25% to about 40% of an omega-3 fattyacid, such as n-3 DHA, (for example, at least 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55% or 60% by weight), and from about 0% to about 3% ofthe omega-3 fatty acid, EPA, (for example, at least 1% or 2% by weight)and from about 4% to about 12% of an omega-6 fatty acid, such as n-6DPA, (for example, at least 4%, 5%, 6%, 7%, 8%, 9%, or 10% by weight).

It is understood that the composition of the lipid produced by theeukaryotic microorganism can be manipulated based on the growingconditions the eukaryotic microorganism exists in. By changing variousparameters, as disclosed herein, the compositions can be manipulated toproduce, for example a better yield of DHA or DPA. For example, themanipulation may not produce more actual grams, but the manipulation,may produce a better ratio of DHA or DPA to EPA and other desired PUFAs,which may be desirable from a purification standpoint. Varyingconditions are discussed herein.

FIG. 10 shows a possible metabolic pathway for the various PUFAsproduced by the disclosed eukaryotic microorganism, consistent withfatty acid methyl ester metabolite tracking. Proteins which can beidentified within the pathways which as disclosed herein are polyketidesynthase, using for example a degenerative primer study, (Metz et al.(2001) Science 293:290-3 and Kaulmann & Hertweck (2002) Angew. Chem.Int. Ed. 41:1866-9). Also elongases and desaturases, using for example ahybridization probe study can be identified. Also fatty acid synthasescan be identified using, for example, a hybridization probe and/or adegenerative primer study.

4. Growing and Culturing

A phenotypic microplate study including carbon; nitrogen (peptidenitrogen); phosphorus and sulfur; osmolytes, and pH was performed.]

An Orthogonal array (Taguchi) method was used to determine optimum mediaconfigurations and variations in nitrogen, carbon and salt concentration(Joseph J & Piganatiells J R (1998) IIE Trans, 20:247-254).

If you increase agitation or dO₂ you increase biomass production & TFAbut decrease DHA. If you decrease agitation or dO₂ you decrease cellularbiomass (g) & decrease TFA but increase DHA but also reduce C16:0, C16:1& C18:1.

If you increase temperature you increase biomass production & TFA butdecrease DHA. If you decrease temperature you decrease cellular biomass(g) & decrease TFA but increase DHA, but reduce C16:0, C16:1 & C18:1.

Cellular biomass derived from the disclosed eukaryotic microorganism canbe obtained by inoculating a suitable natural or artificial seawatermedium, containing from about 2% to about 100% of seawater. Thiseukaryotic microorganism is able to utilize various nutritionalcomponents within this medium. Examples of a carbon source used withinthe medium are carbohydrates such as glucose, fructose, dextrose,lactulose, galactose, maltotriose, maltose, lactose, glycogen, gelatin,starch (corn or wheat) as well as sugar derivatives such as acetate,m-inositol (derived from corn steep liquor), galacturonic acid (derivedfrom pectin), L fucose (derived from galactose), gentiobiose,glucosamine, α-D-glucose-1-phosphate (derived from glucose), cellobiose(derived from cellulose) dextrin (derived from corn) and a-cyclodextrin(derived from starch) and polyols such as maltitol, erythritol, adonitoland oleic acids such as glycerol and tween 80 and amino sugars such asN-acetyl-D-galactosamine, N-acetyl-D-glucosamine andN-acetyl-β-D-mannosamine. While, examples of a nitrogen source arenatural nitrogen sources such as peptone, yeast extract, malt extractand fish meal, or an organic nitrogen sources such as sodium glutamate,but not limited thereto. Furthermore, if necessary phosphates, such aspotassium phosphate, and sodium phosphate, inorganic salts such as,ammonium sulfate, sodium bicarbonate, sodium orthovanadate, potassiumchromate, sodium molybdate, selenous acid, nickel sulfate, coppersulfate, zinc sulfate, cobalt chloride, iron chloride, manganesechloride and calcium chloride may be used as trace nutrients, along withthe chelating compound, ethylenediaminetetraacetic acid, alone or inconjunction with vitamins such as pyridoxine hydrochloride, thiaminehydrochloride, calcium pantothenate, p-aminobenzoic acid, riboflavin,nicotinic acid, biotin, folic acid and vitamin B₁₂. After preparing themedium, the pH is adjusted to between 3.0 and 10.0 using acid or base toadjust where appropriate, for example between pH 4.0 and 6.5, and themedium is sterilized by autoclaving, for example. Cultivation can becarried out for 1 to 30 days, 1 to 21 days, 1 to 15 days, 1 to 12 days,1 to 9 days, or preferably 3 to 5 days at temperatures between 4 to 30°C., preferably 18 to 28° C., by aeration-shaking culture, shakingculture, stationary culture, batch culture, continuous culture, rollingbatch culture, or wave culture, or the like.

The following conditions are an example of conditions that can allow forthe production of a set of lipids in yields which allows for their useas a commodity. Investigation of culture conditions for ONC-T18 revealedthat the eukaryotic microorganism disclosed herein grows well in naturalor artificial sea water or in a medium containing down to 5%concentration of natural or artificial sea water. Carbon and nitrogensources added to the medium may be those conventionally used asdescribed above. The nitrogen source being either natural or organic innature is relatively equal and total nitrogen concentration within themedium is kept constant. These sources are added to the medium atstandard concentrations. If these conditions are met, little influenceon the content of lipid, proportions or the amount of accumulated DHA,DPA and EPA is produced, as disclosed herein.

For high-concentration fermentation of ONC-T18, it is possible to useseveral methods to increase both cellular biomass and lipid productionrates. These include, increasing both the carbon and nitrogenconcentration in the medium (at a ratio of between 6:1 and 15:1,preferably between 6:1 and 13:1 and at temperatures between 4 to 30° C.,preferably 18 to 28° C.) from the range 5 g L⁻¹ to 60 g L⁻¹ to the range100 g L⁻¹ and 160 g L⁻¹ and from the range 4 g L⁻¹ to 10 g L⁻¹ to therange 40 g L⁻¹ to 60 g L⁻¹, respectively. Using this method theproportion of biomass and lipid produced is also increased at comparablerates. Furthermore, it is possible to increase lipid production throughthe use of increased carbon sources from the range 5 g L⁻¹ to 60 g L⁻¹to the range 100 g L⁻¹ and 160 g L⁻¹, while the nitrogen source remainsconstant. Additionally, it is possible to increase biomass productionwhile maintaining lipid content, through the use of increased amounts ofnitrogen sources from the range 10 g L⁻¹ to 60 g L⁻¹ while the carbonsource remains constant. Moreover, experimentation has determined thatbiomass and lipid production greatly increases with increased agitationfrom the range 100 and 1000 rpm, better at between 350 and 600 rpm andoptimal at between 350 and 450 rpm, with only a marginal decrease inlipid content and no decrease in fatty acid profiles, with agitationparticularly relevant at the early stages of heterotrophic fermentation.Experimentation has also determined that lipid production optima areachieved when the dissolved oxygen content of the culture medium isbetween 1 and 10%, optimally at 5%. Finally, the addition of acetate,trace elements, metals and vitamins to the production medium (asmentioned above) increases the production of DHA, EPA and DPA withrespect to other fatty acids without decreasing total lipid values.

By performing heterotrophic fermentation as described above, it ispossible to consistently produce cellular biomass which produces a lipidcontaining the (n-3) series of DHA in a culture of high concentration ofnot less than 5 g and more preferably not less than 20 g/L medium.Furthermore, experimentation has shown that most of these lipidsaccumulate during the later-exponential/transition stages ofcultivation, after maximal biomass levels are reached. Yet, during thefermentation process, lipid content typically does not fall below 25% ofthe total biomass, typically maximizing at around 80%. The cultivationunder the above conditions can be carried out using a conventionalagitation-fermenter. It is also possible to use a bubble columnfermenter (batch or continuous cultures), or a wave fermentor.

Collection of cellular biomass prior to processing for lipid separationcan be performed using various conventional methods such ascentrifugation (such as solid-ejecting centrifuges) or filtration (suchas cross-flow filtration) and may also include the use of aprecipitation agent for the accelerated collection of cellular biomass(such as sodium phosphate, calcium chloride or polyacridamide).

5. Isolation of Lipid

FIG. 7 shows lipid and DHA profiles as functions of a variety ofparameters. All of this data can be used to extract specificcharacteristics about the ONC-T18 eukaryotic microorganism. FIG. 13shows a general fatty acid profile for the disclosed eukaryote.

The fat containing the (n-3) series of DHA and the (n-6) series of DPAcan be obtained by breaking or disrupting the collected cell biomass,for example, via milling, ultrasonication, and then carrying outextraction with a solvent such as chloroform, hexane, methanol, ethanolor via supercritical fluid extraction means. The content of theresultant fat containing the (n-3) series of DHA and the (n-6) series ofDPA per gram of dried cellular biomass is preferably greater than 0.25 gand more preferably greater than 0.6 g.

The disclosed eukaryotic microorganisms, such as ONC-T18, are able toproduce lipid thus obtained, any of its variants and any associationsbetween members of the same species of eukaryotic microorganisms wherebythe lipid profile is as follows. The percentage of neutral lipids can beat least 95% by weight of total lipids. A typical composition of fattyacids for the eukaryotic microorganism, such as ONC-T18, in the neutrallipids is as follows: 15% of myristic acid, 8% of pentadecanoic acid,35% of palmitic acid, 7% of palmitoleic acid, 1% of stearic acid, 2% ofoleic acid, 1% of eicosapentaenoic acid, 6% of docosapentaenoic acid and25% docosahexaenoic acid (GC spectra shown in FIG. 1).

The disclosed eukaryotic microorganisms, such as ONC-T18, are able toproduce lipid thus obtained, any of its variants and any associationsbetween members of the same species of eukaryotic microorganisms wherebythe lipid profile is as follows. The percentage of mono-, di- andtri-glycerides in the neutral lipid fraction of ONC-T18 is 0% to about2%, 0 to about 2% and 96 to about 100%, respectively. While the polarlipid fraction with comprises between 5% and about 10% of the lipidfraction, comprises phosphotidylcholine, phosphotidylserine andphosphotidic acid both bound and unbound to neutral lipids.

It is understood that these lipids can be found in any combination orpermutation within the organism. It is also understood that theconcentrations of these lipids can be manipulated by changing thegrowing conditions and media conditions as discussed herein.

(1) Lipid as Concentration

The eukaryotic microorganism can produce a lipid fraction comprising n-3DHA, EPA and n-6 DPA at greater than or equal to about 4.0 g L⁻¹ ofmedium. The eukaryotic microorganism can produce a lipid compositioncomprising n-3 DHA, EPA and n-6 DPA at greater than or equal to about20.0 g L⁻¹ of medium. The eukaryotic microorganism can produce a lipidcomposition comprising n-3 DHA, EPA and n-6 DPA at greater than or equalto about 14.0 g L⁻¹ of medium. The eukaryotic microorganism can producefrom about 1.5 g L⁻¹ to about 5.0 g L⁻¹ (e.g., about 4.6 g L⁻¹) of then-3 DHA, from about 0.5 g L⁻¹ to about 1.5 g L⁻¹ (e.g., about 0.22 gL⁻¹) of the n-3 EPA, and from about 0.5 g L⁻¹ to about 1.5 g L⁻¹ of then-6 DPA. Furthermore, the eukaryotic microorganism can produce a lipidfraction comprising myristic, myristoleic, pentadecanoic, palmitic,palmitoleic, stearic oleic, linoleic, eicosadienoic, arachidonic,eicosapentaenoic, docosahexanoic and docosapentaenoic acids between301.2 and 360.3 mg g⁻¹ or even up to 790 mg g⁻¹ of cellular biomass. Theeukaryotic microorganism can also produce a fraction comprising between44.3 and 57 mg g⁻¹ myristic acid (equal to 1134.5 to 1458.1 mg L⁻¹), 0.5to 0.65 myristoleic acid (equal to 13.3 to 16.63 mg L⁻¹), 33.5 to 34.6mg g⁻¹ pentadecanoic acid (equal to 856.9 to 885.1 mg L⁻¹), 121.9 and165.1 mg g⁻¹ palmitic acid (equal to 3118.2 to 4223.3 mg L⁻¹), 7.9 to28.5 mg g⁻¹ palmitoleic acid (equal to 202.1 to 729 mg L⁻¹), 4.38 to 5.9mg g⁻¹ stearic acid (equal to 112 to 151 mg L⁻¹), 6.94 to 9.9 mg g⁻¹oleic acid (equal to 177.5 to 253.2 mg L⁻¹), 0.4 to 1.3 mg g⁻¹ linoleicacid (equal to 11.26 to 33.3 mg L⁻¹), 0.5 to 1.0 mg g⁻¹ eicosadienoicacid (equal to 12.8 to 25.6 mg L⁻¹), 0.4 to 0.5 mg g⁻¹ arachidonic acid(equal to 10.2 to 13 mg L⁻¹), 75 to 100 mg g⁻¹ docosahexanoic acid(equal to 1918 to 2560 mg L⁻¹), 1.9 to 6 mg g⁻¹ eicosapentaenoic acid(equal to 48.6 to 153.5 mg L⁻¹) and 17.1 to 33.7 mg g⁻¹ docosapentaenoicacid (equal to 437.4 to 862.1 mg L⁻¹), having a total fatty acid contentwithin the cellular biomass of between 301 to 790 mg g⁻¹ (equal to 7700to 20,209 mg L⁻¹).

(2) Other Molecules

The eukaryotic microorganism can further produce carotenoids andxanthophylls. Examples of such carotenoids and xanthophylls includebeta-carotene, lycopene, astaxanthin, canthaxanthin, phoenicoxanthin,zeaxanthin, echinenone, beta-cryptoxanthin, capsanthin, lutin, annatto,beta-apo-8-carotenal and beta-apo-8-carotenal-ester.

The xanthophylls produced by the disclosed eukaryotic microorganisms canbe conjugated with the various PUFAs also produced by the disclosedeukaryotic microorganisms.

(a) Antioxidants

Generally, antioxidants are compounds that react with, and typically getconsumed by oxygen. Since antioxidants typically react with oxygen,antioxidants also typically react with the free radical generators, andfree radicals. (“The Antioxidants—The Nutrients that Guard Your Body” byRichard A. Passwater, Ph. D., 1985, Keats Publishing Inc., which isherein incorporated by reference at least for material related toantioxidants). The compositions can contain any antioxidants, and anon-limiting list would included but not be limited to, non flavonoidantioxidants and nutrients that can directly scavenge free radicalsincluding multi carotenes, beta-carotenes, alpha-carotenes,gamma-carotenes, lycopene, lutein and zeaxanthins, selenium, Vitamin E,including alpha-, beta- and gamma-(tocopherol, particularlyalpha-tocopherol, etc., vitamin E succinate, and trolox (a solubleVitamin E analog) Vitamin C (ascorbic acid) and Niacin (Vitamin B₃,nicotinic acid and nicotinamide), Vitamin A, 13-cis 30 retinoic acid,N-acetyl-L-cysteine (NAC), sodium ascorbate,pyrrolidin-edithio-carbamate, and coenzyme Q₁₀; enzymes which catalyzethe destruction of free radicals including peroxidases such asglutathione peroxidase (GSHPX) which acts on H₂O₂ and such as organicperoxides, including catalase (CAT) which acts on H₂O₂, superoxidedismutase (SOD) which disproportionates O₂H₂O₂, glutathione transferase(GSHTx), glutathione reductase (GR), glucose 6-phosphate dehydrogenase(G6PD), and mimetics, analogs and polymers thereof (analogs and polymersof antioxidant enzymes, such as SOD, are described in, for example, U.S.Pat. No. 5,171,680 which is incorporated herein by reference formaterial at least related to antioxidants and antioxidant enzymes);glutathione; ceruloplasmin; cysteine, and cysteamine(beta-mercaptoethylamine) and flavenoids and flavenoid like moleculeslike folic acid and folate. A review of antioxidant enzymes and mimeticsthereof and antioxidant nutrients can be found in Kumar et al, Pharmac.Ther. 39: 301, 1988 and Machlin L. J. and Bendich, FASEB Journal1:441-445, 1987 which are incorporated herein by reference for materialrelated to antioxidants.

Flavonoids, also known as “phenylchromones,” are naturally occurring,water-soluble compounds which have antioxidant characteristics.Flavonoids are widely distributed in vascular plants and are found innumerous vegetables, fruits and beverages such as tea and wine(particularly red wine). Flavonoids are conjugated aromatic compounds.The most widely occurring flavonoids are flavones and flavonols (forexample, myricetin, (3,5,7,3′,4′,5′,-hexahydroxyflavone), quercetin(3,5,7,3′,4′-pentahydroxyflavone), kaemferol(3,5,7,4′-tetrahydroxyflavone), and flavones apigenin(5,7,4′-trihydroxyflavone) and luteolin (5,7,3′,4′-tetrahydroxyflavone)and glycosides thereof and quercetin).

Carotenoids are important natural pigments produced by manymicroorganisms and plants, usually red, orange or yellow in color.Traditionally, carotenoids have been used in the feed, food andnutraceutical industries. They are known to be essential for plantgrowth and photosynthesis, and are a main dietary source of vitamin A inhumans. Dietary antioxidants, such as carotenoids (beta-carotene,lycopene, astaxanthin, canthaxanthin, zeaxanthin, capsanthin, lutein,annatto, beta-apo-8-carotenal and beta-apo-8-carotenal-ester), exhibitsignificant anticancer activities and play an important role in theprevention of chronic diseases. Carotenoids are potent biologicalantioxidants that can absorb the excited energy of singlet oxygen ontothe carotenoid chain, leading to the degradation of the carotenoidmolecule but preventing other molecules or tissues from being damaged.

Oxygen is required for metabolic functions, but it also presentschallenges to cells. The human organism has a wide range of metabolicenzymes and antioxidants to rid its cells of oxygen derived molecules.This oxidative stress is supposed to be a contributing factor inconditions such as rheumatoid arthritis, ischemic heart disease andstroke, Alzheimer's dementia, cancer and ageing. Therefore, antioxidantshave the potential to protect against a wide spectrum of diseases.Several antioxidant compounds have been isolated from marine microbialsources; these include astaxanthin, beta-carotene and other carotenoids.

Carotenoids are a widely distributed group of naturally occurringpigments, with over 700 natural lipid-soluble pigments primarilyproduced by microalgal, macroalgal, bacterial and fungal species, withastaxanthin and its derivatives being of particular interestcommercially. Astaxanthin is an extremely effective antioxidantprotector. Yet, unlike beta-carotene, astaxanthin readily crosses theblood-brain/retina barrier, and therefore also has potential to protectfrom diseases of the brain and the eyes. Preclinical studies suggestvarious beneficial effects of consuming astaxanthin such as: (i) inhibitcancer formation and growth in the bladder, colon, liver, mammary andthe oral cavity; (ii) protect the retina of the eye from oxidativedamage and thus has an effect against age related macular disease; (iii)promote increased immune activity, (iv) provide protection fromultraviolet light damage, as well as (v) provide increased muscleendurance.

(b) Isolation of Microorganisms

Disclosed are microorganisms from the family Thraustochytriaceaeobtained by a method comprising baiting a vegetative sample in saltwater (natural sea or artificial) with pollen grains and incubating;separating and transferring the grains to a heterotrophic medium andincubating; identifying an isolate that produces fatty acids, isolatingfrom the identified isolate the microorganism from the familyThraustochytriaceae. Additional forms of isolation include mediasupplemented with appropriate antibiotics and identification via eitherby microscopic means as mentioned above or via the use of 18S rRNA geneprimers or probes. The heterotrophic medium can be as described below.

6. Lipids and Other Molecules Produced by the Eukaryotic Microorganism

Disclosed are lipid compositions comprising from about 25 wt. % to about40 wt. % of n-3 DHA, from about 6 wt. % to about 10 wt. % of n-6 DPA,and from about 0 wt. % to about 3 wt. % of n-3 EPA.

The lipid composition can further comprise from about 11 wt. % to about15 wt. % (e.g., about 13 wt. %) myristic acid, from about 7 wt. % toabout 11 wt. % (e.g., about 9 wt. %) pentadecanoic acid, from about 37wt. % to about 41 wt. % (e.g., about 39 wt. %) palmitic acid, from about3 wt. % to about 7 wt. % (e.g., about 5 wt. %) palmitoleic acid, fromabout 0 to about 3 wt. % (e.g., about 1 wt. %) stearic acid, or fromabout 1 wt. % to about 4 wt. % (e.g., about 2 wt. %) oleic acid.

The lipid composition can comprise n-3 DHA in concentrations in excessof about 400 mg of biomass, n-6 DPA in concentrations in excess of 100mg of biomass.

The lipid composition can further comprise carotenoids. Examples of suchcarotenoids include beta-carotene, lycopene, astaxanthin, zeaxanthin,canthaxanthin, echinenone, phoenicoxanthin, capsanthin, lutein, annatto,beta-apo-8-carotenal, and beta-apo-8-carotenal-ester.

In one aspect, the composition can comprise at least about 24 wt. % n-3DHA, about 1 wt. % n-3 DPA, about 6 wt. % n-6 DPA, and about 1 wt. % n-3EPA.

7. Composition Containing the Molecules Produced by the EukaryoticMicroorganism

A foodstuff, supplement, pharmaceutical composition for both human andanimal (including marine) can comprise the composition (lipid, lipidwith antioxidant and antioxidant alone).

Also disclosed is an infant formula comprising the composition (lipid,lipid with antioxidant and antioxidant alone).

C. METHODS

1. Methods of Making Lipids

Disclosed are methods of preparing a lipid composition, the methodcomprising: culturing a eukaryotic microorganism comprising one or moremicroorganisms from the family Thraustochytriaceae, and isolating thelipid composition.

A variety of procedures can be employed in the recovery of the resultantcellular biomass from fermentation in various culture media, such as byfiltration or centrifugation. The cells can then be washed, frozen,lyophilized, or spray dried, and stored under a non-oxidizing atmosphereto eliminate the presence of oxygen, prior to incorporation into aprocessed food or feed product.

Cellular lipids containing the (n-3) DHA, EPA and (n-6) DPA PUFAs canalso be extracted from the cellular biomass methods such assupercritical fluid extraction, or by extraction with solvents such aschloroform, hexane, methylene chloride, or methanol, and the resultingextract evaporated under negative pressure to produce a sample ofconcentrated lipid material. The omega-3 and omega-6 PUFAs may befurther concentrated by hydrolyzing the lipids and concentrating thehighly unsaturated fraction by employing traditional methods such asurea adduction or fractional distillation, column chromatography, or bysupercritical fluid fractionation. The cells can also be broken or lysedand the lipids extracted into vegetable or animal (e.g. fish oils) oils.The extracted oils can be refined by well-known processes routinelyemployed to refine vegetable oils (e.g. by chemical or physicalrefining). These refining processes remove impurities from extractedoils before they are used or sold as edible oils. After refining, theoils can be used directly as a feed or food additive to produce omega-3and/or omega-6 enriched products. Alternatively, the oil can be furtherprocessed and purified as outlined below and then used in the aboveapplications and also in pharmaceutical applications.

In another process for the production of enriched (concentrated) omega-3or omega-6 oils, the harvested cellular biomass (fresh or dried) can beruptured or permeabilized by well-known techniques such as sonication,liquid-shear disruption methods, bead milling, pressing under highpressure, freeze-thawing, or enzymatic digestion of the cell wall. Thelipids from the ruptured cells are extracted by use of a solvent ormixture of solvents such as hexane, chloroform, ether, or methanol. Thesolvent is removed and the lipids hydrolyzed by using any of thewell-known methods for converting triglycerides to free fatty acids oresters of fatty acids including base, acid, or enzymatic hydrolysis.After hydrolysis is completed, the nonsaponifiable compounds areextracted into a solvent such as ether, hexane or chloroform andremoved. The remaining solution is then acidified by addition of anacid, and the free fatty acid extracted into a solvent such as hexane,ether or chloroform. The solvent solution containing the free fattyacids can then be cooled to a temperature low enough for crystallizationof the non PUFA compounds, which can then be removed via filtration,centrifugation or settling. Resulting in the concentration of theremaining PUFA compounds and used as a nutritional supplements forhumans, as a food additive, or as pharmaceutical applications.

Also, disclosed is a lipid composition prepared by the method disclosedabove.

The microorganisms from the family Thraustochytriaceae can be any of themicroorganisms disclosed above.

a) Medium

The heterotrophic medium can comprise sea salt (artificial or natural),one or more carbon sources, and one or more nitrogen sources. The seasalt can be present in an amount of from about 2.0 to about 40.0 g L⁻¹.The concentration of the carbon and nitrogen source used under standardcultivation conditions (not for high-concentration, but rather costefficient fermentation) falls within the range of 5 g L⁻¹ to 60 g L⁻¹and 4 g L⁻¹ to 10 g L⁻¹, respectively. For high-concentrationfermentation, the concentration of the carbon and nitrogen source usedunder standard cultivation conditions falls within the range of 100 gL⁻¹ and 160 g L⁻¹ and 40 g L⁻¹ to 60 g L⁻¹, respectively. The trendbeing that for oil accumulation, the eukaryotic microorganism is grownin a culture medium (as those described above) in which the supply ofnitrogen is limited after about 24 to about 48 hours, while the supplyof carbon remains in abundance. This eukaryotic microorganism continuesto assimilate the carbon (in the form of simple sugars) but can nolonger undergo cell division due to a lack of nitrogen for thegeneration of relevant proteins and nucleic acids. The result being thatthese sugars are converted into storage oils, much in the same way thatRatledge C. (Lipid Tech. 16:34-39, 2004) describes and FIG. 9 depictsthis phenomenon specific for this organism.

The nitrogen source can be one or more of peptone, yeast extract, maltextract, and sodium glutamate. The nitrogen source can also be cornsteep liquor or cotton seed extract. The nitrogen source can compriseyeast extract and/or peptone or monosodium glutamate. For example, thenitrogen source can include, but is not limited to EMD™ YE-MSG, EMD™ YE,EMD™ Peptone-MSG, Sigma™ YE-MSG, Sigma™ YE, Fermtech™ YE-MSG, Fermtech™YE, or Fish meal (62% protein). The yeast extract can be present in anamount of about 2 g L⁻¹. The monosodium glutamate can be present in anamount of about 8 g L⁻¹.

The carbon source can be one or more of D-trehalose, glycerol,D-gluconic acid, L lactic acid, D,L-malic acid, D-ribose, Tween 20,D-fructose, acetate, acetic acid, alpha-D-glucose, maltose, thymidine,L-asparagine, D-xylose, Tween 40, a-keto-glutaric acid, sucrose,L-glutamine, Tween 80, beta-methyl-D-glucoside, maltotriose,adenosinine, fumaric acid, bromo succinic acid, L-serine, D-cellobiose,L-alanyl-glycine, methyl pyruvate, L-malic acid, glycyl-L proline,D-palcose, L-lyxose, pyruvic acid, alpha-D-lactose, dextrin,D-arabinose, 2-deoxy-D ribose, gelatin, dextrose, starch,3-O-beta-D-galactopyranosyl-D-arabinose, D-tagatose, 5-keto-D-gluconicacid, oxalomalic acid, sorbic acid, L-ornithine, and dihydroxy acetate.In one aspect, the carbon source can be D,L-malic acid, D-fructose,D-xylose, fumaric acid, D-cellobiose, 5-keto-D-gluconic acid, pyruvicacid, alpha-D-lactose, corn dextrin, gelatin, corn starch or wheatstarch. The carbon source can be present in an amount of from about 1 gL⁻¹ to about 60 g L⁻¹ and up to about 200 g L⁻¹.

In one example, the medium can comprise about 5 g D-glucose, about 2 gpeptone, and about 2 g yeast extract per liter of salt water (natural orartificial). In another, the medium can comprise about 60 g D-glucose,about 10 g yeast extract per liter of salt water (natural orartificial). In another, the medium can comprise about 8 g yeastextract, 32 g MSG, 24 g sea salt (natural and artificial) and 300 gD-glucose per liter.

The medium can further comprise phosphates (e.g., potassium phosphateand sodium phosphates). The medium can further comprise inorganic salts(e.g., ammonium sulfate, sodium bicarbonate, sodium orthovanadate,potassium chromate, sodium molybdate, selenous acid, nickel sulfate,copper sulfate, zinc sulfate, cobalt chloride, iron chloride, manganesechloride). The medium can further comprise a chelating compound (e.g.,EDTA). The medium can further comprise vitamins (e.g., pyridoxinehydrochloride, thiamin hydrochloride, calcium pantothenate,p-aminobenzoic acid, riboflavin, nicotinic acid, biotin, folic acid, andvitamin B₁₂). The medium can be at a pH of from about 4.0 to about 6.5.

Incubation can be from about 1 to about 9 days (e.g., from about 3 toabout 5 days). Incubation can be at from about 18 to about 30° C. (e.g.,from about 18-25° C.). Incubation can further comprise shaking oraeration.

Isolating the lipid can comprise contacting the microorganisms with anextraction solvent. The solvent can comprise one or more solvents chosenfrom chloroform, hexane, methanol, or ethanol, or supercritical CO₂.

The method can produce any of the compositions as disclosed above.

The eukaryotic microorganism can produce a lipid composition comprisingn-3 DHA at greater than or equal to about 20 g L⁻¹ of medium. Theeukaryotic microorganism can produce a lipid composition comprising n-3DHA at greater than or equal to about 40 g L⁻¹ of medium. The eukaryoticmicroorganism can produce a lipid composition comprising n-3 DHA atgreater than or equal to about 80 g L⁻¹ of medium.

2. Screening and Identification Methods

The eukaryotic microorganism as disclosed herein can produce a lipidcontaining the (n-3) series of docosahexaenoic acid and eicosapentaenoicacid and the (n-6) series of DPA. These eukaryotic microorganism can beselected, for example, with the following screening method. Vegetativesamples can be (and were) placed in 20 mL vials containing 10 mL ofsterile 0.2 μm filtered natural seawater containing penicillin andstreptomycin at 300 and 500 mg L⁻¹, respectively. The vials were thenbaited with sterile pollen grains and incubated for 48 hours at 18 to25° C. The pollen grains were then transferred onto agar platescontaining antibiotics (as above) and incubated under the sameconditions. Single, irregular, hyaline colonies made up of spherical orlimaciform cells and atypical of either yeast or bacterial colonies werepicked and sub-cultured on the same medium and under the same conditionsas above. These isolates were then screened for growth and fatty acidsusing a nutrient liquid medium, prepared with 0.2 μm filtered naturalseawater containing 5 g L⁻¹ glucose, 2 g L⁻¹ peptone and 2 g L⁻¹ yeastextract, with the resulting cellular biomass collected by centrifugationor sedimentation within a liquid medium. Fatty acids were directlytransesterified using conventional methods, with the fatty acid methylester composition analyzed via gas chromatography, with strains thatproduce appropriate amounts of the n-3 series of DHA and the n-6 seriesof DPA selected for further work.

Disclosed are methods of identifying an eukaryotic microorganism, themethod comprising: baiting a vegetative sample in salt water (naturalsea or artificial) with pollen grains and incubating; transferring thegrains to a heterotrophic medium and incubating; and identifyingisolates that produce fatty acids.

Also disclosed are lipid compositions produced by the above identifiedeukaryotic microorganisms.

Also disclosed are lipid compositions produced by methods using thedisclosed eukaryotic microorganisms and the methods disclosed herein.

Also disclosed are eukaryotic microorganisms (ONC-T18) having AmericanType Culture Collection accession number PTA-6245.

Also disclosed are eukaryotic microorganisms belonging to the orderThraustochytriales (ONC-T18) having 18S rRNA, such as SEQ ID 1, andidentified as a Thraustochytrium sp.

Also disclosed is a eukaryotic microorganism, Thraustochytrium sp.capable of producing DHA and DPA in concentrations in excess of 400 mgL⁻¹ and 100 mg L⁻¹, respectively.

Also disclosed is a eukaryotic microorganism, Thraustochytrium sp.capable of producing carotenoids via heterotrophic fermentation asmentioned above in the range 50 to 1250 mg kg⁻¹ and astaxanthin,zeaxanthin, canthaxanthin, echinenine and beta-carotene in the range of1 to 20 mg kg⁻¹, 0.25 to 10 mg kg⁻¹, 1 to 20 mg kg⁻¹ 1 to 20 mg kg⁻¹ and1 to 200 mg kg⁻¹, respectively.

Also disclosed are processes for growing a eukaryotic microorganismcomprising, culturing the eukaryotic microorganism under conditions,wherein the conditions comprise a medium comprising sodium chloride inthe form of artificial sea salt (trophic marine) between 2.0 and 15.0 gL⁻¹; a nitrogen source in the form of yeast extract and monosodiumglutamate at 2.0 and 8.0 g L⁻¹ respectively; and carbon in the form ofglucose up to 130 g L⁻¹.

The disclosed processes can, for example, grow ONC-T18, whereby at least24% weight is DHA, at least 6% by weight is DPA and at least 1% is EPAof total fatty acid.

The disclosed processes for growth can also, for example, grow ONC-T18such that at least 1% by weight is carotenoid material, with from 1 to2% and at least 1.2% of that being astaxanthin, with from 0.25 and 1%and at least 0.45% being zeaxanthin, with from 5 to 16% and at least 9%being canthaxanthin, with from 1 to 2% and at least 1.2% of that beingechinenone and from 12 to 16% and at least 14% by weight beingbeta-carotene.

3. Nucleic Acids

There are a variety of molecules disclosed herein that are nucleic acidbased, including for example the nucleic acids that encode, for example,rRNA, as well as any other proteins disclosed herein, as well as variousfunctional nucleic acids. The disclosed nucleic acids are made up of forexample, nucleotides, nucleotide analogs, or nucleotide substitutes.Non-limiting examples of these and other molecules are discussed herein.It is understood that for example, when a vector is expressed in a cell,that the expressed mRNA will typically be made up of A, C, G, and U/T.Likewise, it is understood that if, for example, an antisense moleculeis introduced into a cell or cell environment through for exampleexogenous delivery, it is advantageous that the antisense molecule bemade up of nucleotide analogs that reduce the degradation of theantisense molecule in the cellular environment.

a) Nucleotides and Related Molecules

A nucleotide is a molecule that contains a base moiety, a sugar moietyand a phosphate moiety. Nucleotides can be linked together through theirphosphate moieties and sugar moieties creating an internucleosidelinkage. The base moiety of a nucleotide can be adenin-9-yl (A),cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T).The sugar moiety of a nucleotide is a ribose or a deoxyribose. Thephosphate moiety of a nucleotide is pentavalent phosphate. Annon-limiting example of a nucleotide would be 3′-AMP (3′-adenosinemonophosphate) or 5′-GMP (5′-guanosine monophosphate).

A nucleotide analog is a nucleotide which contains some type ofmodification to either the base, sugar, or phosphate moieties.Modifications to nucleotides are well known in the art and would includefor example, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine,xanthine, hypoxanthine, and 2-aminoadenine as well as modifications atthe sugar or phosphate moieties.

Nucleotide substitutes are molecules having similar functionalproperties to nucleotides, but which do not contain a phosphate moiety,such as peptide nucleic acid (PNA). Nucleotide substitutes are moleculesthat will recognize nucleic acids in a Watson-Crick or Hoogsteen manner,but which are linked together through a moiety other than a phosphatemoiety. Nucleotide substitutes are able to conform to a double helixtype structure when interacting with the appropriate target nucleicacid.

It is also possible to link other types of molecules (conjugates) tonucleotides or nucleotide analogs to enhance for example, cellularuptake. Conjugates can be chemically linked to the nucleotide ornucleotide analogs. Such conjugates include but are not limited to lipidmoieties such as a cholesterol moiety. (Letsinger et al., Proc. Natl.Acad. Sci. USA, 86:6553-6556, 1989),

A Watson-Crick interaction is at least one interaction with theWatson-Crick face of a nucleotide, nucleotide analog, or nucleotidesubstitute. The Watson-Crick face of a nucleotide, nucleotide analog, ornucleotide substitute includes the C2, N1, and C6 positions of a purinebased nucleotide, nucleotide analog, or nucleotide substitute and theC2, N3, C4 positions of a pyrimidine based nucleotide, nucleotideanalog, or nucleotide substitute.

A Hoogsteen interaction is the interaction that takes place on theHoogsteen face of a nucleotide or nucleotide analog, which is exposed inthe major groove of duplex DNA. The Hoogsteen face includes the N7position and reactive groups (NH2 or O) at the C6 position of purinenucleotides.

b) Sequences

There are a variety of sequences related to, for example, SEQ ID NO:1,as well as any other nucleic acids and proteins disclosed herein thatcan be disclosed on Genbank, and these sequences and others are hereinincorporated by reference in their entireties as well as for individualsubsequences contained therein.

A variety of sequences are provided herein and these and others can befound in Genbank, at www.pubmed.gov. Those of skill in the artunderstand how to resolve sequence discrepancies and differences and toadjust the compositions and methods relating to a particular sequence toother related sequences. Primers and/or probes can be designed for anysequence given the information disclosed herein and known in the art.

c) Primers and Probes

Disclosed are compositions including primers and probes, which arecapable of interacting with the genes disclosed herein. In certainembodiments the primers are used to support DNA amplification reactions.Typically the primers will be capable of being extended in a sequencespecific manner. Extension of a primer in a sequence specific mannerincludes any methods wherein the sequence and/or composition of thenucleic acid molecule to which the primer is hybridized or otherwiseassociated directs or influences the composition or sequence of theproduct produced by the extension of the primer. Extension of the primerin a sequence specific manner therefore includes, but is not limited to,PCR, DNA sequencing, DNA extension, DNA polymerization, RNAtranscription, or reverse transcription. Techniques and conditions thatamplify the primer in a sequence specific manner are preferred. Incertain aspects the primers may be used as species or genus specificprobes for the Thraustochytrium or Bacillus mentioned here. In thisinstance, primers would be designed to be specific to the eukaryoticmicroorganism, with PCR reactions subsequently carried out. Presence oftarget species would then be determined by successful PCR productformation. In certain aspects the primers can also be used for DNAamplification reactions, such as PCR or direct sequencing. It isunderstood that in certain aspects the primers can also be extendedusing non-enzymatic techniques, where for example, the nucleotides oroligonucleotides used to extend the primer are modified such that theywill chemically react to extend the primer in a sequence specificmanner. Typically the disclosed primers hybridize with the nucleic acidor region of the nucleic acid or they hybridize with the complement ofthe nucleic acid or complement of a region of the nucleic acid.

d) Nucleic Acid Delivery

In the methods described above which include the administration anduptake of exogenous DNA into the cells of a subject (i.e., genetransduction or transfection), the disclosed nucleic acids can be in theform of naked DNA or RNA, or the nucleic acids can be in a vector fordelivering the nucleic acids to the cells, whereby the antibody-encodingDNA fragment is under the transcriptional regulation of a promoter, aswould be well understood by one of ordinary skill in the art. The vectorcan be a commercially available preparation, such as an adenovirusvector (Quantum Biotechnologies, Inc. (Laval, Quebec, Canada). Deliveryof the nucleic acid or vector to cells can be via a variety ofmechanisms. As one example, delivery can be via a liposome, usingcommercially available liposome preparations such as LIPOFECTIN,LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, Md.), SUPERFECT (Qiagen,Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison,Wis.), as well as other liposomes developed according to proceduresstandard in the art. In addition, the disclosed nucleic acid or vectorcan be delivered in vivo by electroporation, the technology for which isavailable from Genetronics, Inc. (San Diego, Calif.) as well as by meansof a SONOPORATION machine (ImaRx Pharmaceutical Corp., Tucson, Ariz.).

As one example, vector delivery can be via a viral system, such as aretroviral vector system which can package a recombinant retroviralgenome (see e.g., Pastan et al., Proc. Natl. Acad. Sci. U.S.A. 85:4486,1988; Miller et al., Mol. Cell. Biol. 6:2895, 1986). The recombinantretrovirus can then be used to infect and thereby deliver to theinfected cells nucleic acid encoding a broadly neutralizing antibody (oractive fragment thereof). The exact method of introducing the alterednucleic acid into mammalian cells is, of course, not limited to the useof retroviral vectors. Other techniques are widely available for thisprocedure including the use of adenoviral vectors (Mitani et al., Hum.Gene Ther. 5:941-948, 1994), adeno-associated viral (AAV) vectors(Goodman et al., Blood 84:1492-1500, 1994), lentiviral vectors (Naidiniet al., Science 272:263-267, 1996), pseudotyped retroviral vectors(Agrawal et al., Exper. Hematol. 24:738-747, 1996). Physicaltransduction techniques can also be used, such as liposome delivery andreceptor-mediated and other endocytosis mechanisms (see, for example,Schwartzenberger et al., Blood 87:472-478, 1996). This disclosedcompositions and methods can be used in conjunction with any of these orother commonly used gene transfer methods.

4. Expression Systems

The nucleic acids that are delivered to cells typically containexpression controlling systems. For example, the inserted genes in viraland retroviral systems usually contain promoters, and/or enhancers tohelp control the expression of the desired gene product. A promoter isgenerally a sequence or sequences of DNA that function when in arelatively fixed location in regard to the transcription start site. Apromoter contains core elements required for basic interaction of RNApolymerase and transcription factors, and may contain upstream elementsand response elements.

It is understood that there are a variety of transcription controlsystems that can be used in the organisms disclosed herein, in additionto the general systems discussed below. It is understood that theorganisms disclosed herein can be transfected and transformed with avariety of genes, such as marker genes, as discussed herein, or geneswhich have other desirable attributes, such as enhanced or unique growthcharacteristics.

a) Viral Promoters and Enhancers

Preferred promoters controlling transcription from vectors in mammalianhost cells may be obtained from various sources, for example, thegenomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus,retroviruses, hepatitis-B virus and most preferably cytomegalovirus, orfrom heterologous mammalian promoters, e.g. beta actin promoter. Theearly and late promoters of the SV40 virus are conveniently obtained asan SV40 restriction fragment which also contains the SV40 viral originof replication (Fiers et al., Nature, 273:113, 1978). The immediateearly promoter of the human cytomegalovirus is conveniently obtained asa HindIII E restriction fragment (Greenway, P. J. et al., Gene18:355-360, 1982). Of course, promoters from the host cell or relatedspecies also are useful herein.

Enhancer generally refers to a sequence of DNA that functions at nofixed distance from the transcription start site and can be either 5′(Laimins, L. et al., Proc. Natl. Acad. Sci. 78:993, 1981) or 3′ (Lusky,M. L., et al., Mol. Cell. Bio. 3:1108, 1983) to the transcription unit.Furthermore, enhancers can be within an intron (Banerji, J. L. et al.,Cell 33:729, 1983) as well as within the coding sequence itself(Osborne, T. F., et al., Mol. Cell. Bio. 4:1293, 1984). They are usuallybetween 10 and 300 bp in length, and they function in cis. Enhancersfunction to increase transcription from nearby promoters. Enhancers alsooften contain response elements that mediate the regulation oftranscription. Promoters can also contain response elements that mediatethe regulation of transcription. Enhancers often determine theregulation of expression of a gene. While many enhancer sequences arenow known from mammalian genes (globin, elastase, albumin,alpha-fetoprotein and insulin), typically one will use an enhancer froma eukaryotic cell virus for general expression. Preferred examples arethe SV40 enhancer on the late side of the replication origin (100-270bp), the cytomegalovirus early promoter enhancer, the polyoma enhanceron the late side of the replication origin, and adenovirus enhancers.

The promoter and/or enhancer may be specifically activated either bylight or specific chemical events which trigger their function. Systemscan be regulated by reagents such as tetracycline and dexamethasone.There are also ways to enhance viral vector gene expression by exposureto irradiation, such as gamma irradiation, or alkylating chemotherapydrugs.

In certain embodiments the promoter and/or enhancer region can act as aconstitutive promoter and/or enhancer to maximize expression of theregion of the transcription unit to be transcribed. In certainconstructs the promoter and/or enhancer region be active in alleukaryotic cell types, even if it is only expressed in a particular typeof cell at a particular time. A preferred promoter of this type is theCMV promoter (650 bp). Other preferred promoters are SV40 promoters,cytomegalovirus (full length promoter), and retroviral vector LTF.

It has been shown that all specific regulatory elements can be clonedand used to construct expression vectors that are selectively expressedin specific cell types such as melanoma cells. The glial fibrillaryacetic protein (GFAP) promoter has been used to selectively expressgenes in cells of glial origin.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect,plant, animal, human or nucleated cells) may also contain sequencesnecessary for the termination of transcription which may affect mRNAexpression. These regions are transcribed as polyadenylated segments inthe untranslated portion of the mRNA encoding tissue factor protein. The3′ untranslated regions also include transcription termination sites. Itis preferred that the transcription unit also contain a polyadenylationregion. One benefit of this region is that it increases the likelihoodthat the transcribed unit will be processed and transported like mRNA.The identification and use of polyadenylation signals in expressionconstructs is well established. It is preferred that homologouspolyadenylation signals be used in the transgene constructs. In certaintranscription units, the polyadenylation region is derived from the SV40early polyadenylation signal and consists of about 400 bases. It is alsopreferred that the transcribed units contain other standard sequencesalone or in combination with the above sequences improve expressionfrom, or stability of, the construct.

b) Markers

The viral vectors can include nucleic acid sequence encoding a markerproduct. This marker product is used to determine if the gene has beendelivered to the cell and once delivered is being expressed. Preferredmarker genes are the E. coli lacZ gene, which encodes β-galactosidase,and green fluorescent protein.

In some embodiments the marker may be a selectable marker. Examples ofsuitable selectable markers for mammalian cells are dihydrofolatereductase (DHFR), thymidine kinase, neomycin, neomycin analog G418,hydromycin, and puromycin. When such selectable markers are successfullytransferred into a mammalian host cell, the transformed mammalian hostcell can survive if placed under selective pressure. There are twowidely used distinct categories of selective regimes. The first categoryis based on a cell's metabolism and the use of a mutant cell line whichlacks the ability to grow independent of a supplemented media. Twoexamples are: CHO DHFR-cells and mouse LTK-cells. These cells lack theability to grow without the addition of such nutrients as thymidine orhypoxanthine. Because these cells lack certain genes necessary for acomplete nucleotide synthesis pathway, they cannot survive unless themissing nucleotides are provided in a supplemented media. An alternativeto supplementing the media is to introduce an intact DHFR or TK geneinto cells lacking the respective genes, thus altering their growthrequirements. Individual cells which were not transformed with the DHFRor TK gene will not be capable of survival in non-supplemented media.

The second category is dominant selection which refers to a selectionscheme used in any cell type and does not require the use of a mutantcell line. These schemes typically use a drug to arrest growth of a hostcell. Those cells which have a novel gene would express a proteinconveying drug resistance and would survive the selection. Examples ofsuch dominant selection use the drugs neomycin, (Southern P. and Berg,P., J. Molec. Appl. Genet. 1:327, 1982), mycophenolic acid, (Mulligan,R. C. and Berg, P. Science 209:1422, 1980) or hygromycin, (Sugden, B. etal., Mol. Cell. Biol. 5:410-413, 1985). The three examples employbacterial genes under eukaryotic control to convey resistance to theappropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid)or hygromycin, respectively. Others include the neomycin analog G418 andpuramycin.

5. Peptides

a) Protein Variants

As discussed herein there are numerous variants of the disclosedorganism proteins that are known and herein contemplated. In addition,to the known functional Thraustochytriales strain there are derivativesof the Thraustochytriales proteins which also function in the disclosedmethods and compositions. Protein variants and derivatives are wellunderstood to those of skill in the art and in can involve amino acidsequence modifications. For example, amino acid sequence modificationstypically fall into one or more of three classes: substitutional,insertional or deletional variants. Insertions include amino and/orcarboxyl terminal fusions as well as intrasequence insertions of singleor multiple amino acid residues. Insertions ordinarily will be smallerinsertions than those of amino or carboxyl terminal fusions, forexample, on the order of one to four residues. Immunogenic fusionprotein derivatives, such as those described in the examples, are madeby fusing a polypeptide sufficiently large to confer immunogenicity tothe target sequence by cross-linking in vitro or by recombinant cellculture transformed with DNA encoding the fusion. Deletions arecharacterized by the removal of one or more amino acid residues from theprotein sequence. Typically, no more than about from 2 to 6 residues aredeleted at any one site within the protein molecule. These variantsordinarily are prepared by site specific mutagenesis of nucleotides inthe DNA encoding the protein, thereby producing DNA encoding thevariant, and thereafter expressing the DNA in recombinant cell culture.Techniques for making substitution mutations at predetermined sites inDNA having a known sequence are well known, for example M13 primermutagenesis and PCR mutagenesis. Amino acid substitutions are typicallyof single residues, but can occur at a number of different locations atonce; insertions usually will be on the order of about from 1 to 10amino acid residues; and deletions will range about from 1 to 30residues. Deletions or insertions preferably are made in adjacent pairs,i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions,deletions, insertions or any combination thereof may be combined toarrive at a final construct. The mutations must not place the sequenceout of reading frame and preferably will not create complementaryregions that could produce secondary mRNA structure. Substitutionalvariants are those in which at least one residue has been removed and adifferent residue inserted in its place. Such substitutions generallyare made in accordance with the following Tables 1 and 2 and arereferred to as conservative substitutions.

Substantial changes in function or immunological identity are made byselecting substitutions that are less conservative than those in Table2, i.e., selecting residues that differ more significantly in theireffect on maintaining (a) the structure of the polypeptide backbone inthe area of the substitution, for example as a sheet or helicalconformation, (b) the charge or hydrophobicity of the molecule at thetarget site or (c) the bulk of the side chain. The substitutions whichin general are expected to produce the greatest changes in the proteinproperties will be those in which (a) a hydrophilic residue, e.g. serylor threonyl, is substituted for (or by) a hydrophobic residue, e.g.leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine orproline is substituted for (or by) any other residue; (c) a residuehaving an electropositive side chain, e.g., lysyl, arginyl, or histidyl,is substituted for (or by) an electronegative residue, e.g., glutamyl oraspartyl; or (d) a residue having a bulky side chain, e.g.,phenylalanine, is substituted for (or by) one not having a side chain,e.g., glycine, in this case, (e) by increasing the number of sites forsulfation and/or glycosylation.

TABLE 1 Amino Acid Abbreviations Amino Acid Abbreviations Alanine Ala AArginine Arg R Asparagine Asn N Aspartic acid Asp D Cysteine Cys CGlutamine Gln Q Glutamic acid Glu E Glycine Gly G Histidine His HIsoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met MPhenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr TTryptophan Trp W Tyrosine Tyr Y Valine Val V

TABLE 2 Amino Acid Substitutions Original Residue Exemplary ConservativeSubstitutions* Ala Ser Arg Lys; Gln Asn Gln; His Asp Glu Cys Ser GlnAsn; Lys Glu Asp Gly Pro His Asn; Gln Ile Leu; Val Leu Ile; Val Lys Arg;Gln Met Leu; Ile Phe Met; Leu; Tyr Pro Gly Ser Thr Thr Ser Trp Tyr TyrTrp; Phe Val Ile; Leu *Others are known in the art

For example, the replacement of one amino acid residue with another thatis biologically and/or chemically similar is known to those skilled inthe art as a conservative substitution. For example, a conservativesubstitution would be replacing one hydrophobic residue for another, orone polar residue for another. The substitutions include combinationssuch as, for example, Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser,Thr; Lys, Arg; and Phe, Tyr. Such conservatively substituted variationsof each explicitly disclosed sequence are included within the mosaicpolypeptides provided herein.

Substitutional or deletional mutagenesis can be employed to insert sitesfor N glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr).Deletions of cysteine or other labile residues also may be desirable.Deletions or substitutions of potential proteolysis sites, e.g. Arg, isaccomplished for example by deleting one of the basic residues orsubstituting one by glutaminyl or histidyl residues.

Certain post-translational derivatizations are the result of the actionof recombinant host cells on the expressed polypeptide. Glutaminyl andasparaginyl residues are frequently post-translationally deamidated tothe corresponding glutamyl and asparyl residues. Alternatively, theseresidues are deamidated under mildly acidic conditions. Otherpost-translational modifications include hydroxylation of proline andlysine, phosphorylation of hydroxyl groups of seryl or threonylresidues, methylation of the o-amino groups of lysine, arginine, andhistidine side chains (T. E. Creighton, Proteins: Structure andMolecular Properties, W. H. Freeman & Co., San Francisco pp 79-86,1983), acetylation of the N-terminal amine and, in some instances,amidation of the C-terminal carboxyl.

It is understood that one way to define the variants and derivatives ofthe disclosed proteins herein is through defining the variants andderivatives in terms of homology/identity to specific known sequences.Specifically disclosed are variants of proteins herein disclosed whichhave at least, 60%, 70% or 75% or 80% or 85% or 90% or 95% homology tothe stated sequence. Those of skill in the art readily understand how todetermine the homology of two proteins. For example, the homology can becalculated after aligning the two sequences so that the homology is atits highest level.

Another way of calculating homology can be performed by publishedalgorithms. Optimal alignment of sequences for comparison may beconducted by the local homology algorithm of Smith and Waterman Adv.Appl. Math. 2: 482, 1981, by the homology alignment algorithm ofNeedleman and Wunsch, J. Mol. Biol. 48: 443, 1970, by the search forsimilarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP,BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group, 575 Science Dr., Madison, Wis.), or byinspection.

The same types of homology can be obtained for nucleic acids by forexample the algorithms disclosed in Zuker, M. Science 244:48-52, 1989,Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger etal. Methods Enzymol. 183:281-306, 1989 which are herein incorporated byreference for at least material related to nucleic acid alignment.

It is understood that the description of conservative mutations andhomology can be combined together in any combination, such asembodiments that have at least 70% homology to a particular sequencewherein the variants are conservative mutations.

As this specification discusses various proteins and protein sequencesit is understood that the nucleic acids that can encode those proteinsequences are also disclosed. This would include all degeneratesequences related to a specific protein sequence, i.e. all nucleic acidshaving a sequence that encodes one particular protein sequence as wellas all nucleic acids, including degenerate nucleic acids, encoding thedisclosed variants and derivatives of the protein sequences. Thus, whileeach particular nucleic acid sequence may not be written out herein, itis understood that each and every sequence is in fact disclosed anddescribed herein through the disclosed protein sequence. It is alsounderstood that while no amino acid sequence indicates what particularDNA sequence encodes that protein within an organism, where particularvariants of a disclosed protein are disclosed herein, the known nucleicacid sequence that encodes that protein in the particular strain fromwhich that protein arises is also known and herein disclosed anddescribed.

It is understood that there are numerous amino acid and peptide analogswhich can be incorporated into the disclosed compositions. For example,there are numerous D amino acids or amino acids which have a differentfunctional substituent then the amino acids shown in Table 1 and Table2. The opposite stereo isomers of naturally occurring peptides aredisclosed, as well as the stereo isomers of peptide analogs. These aminoacids can readily be incorporated into polypeptide chains by chargingtRNA molecules with the amino acid of choice and engineering geneticconstructs that utilize, for example, amber codons, to insert the analogamino acid into a peptide chain in a site specific way (Thorson et al.,Methods in Mol. Biol. 77:43-73, 1991, Zoller, Curr. Opin. Biotech.,3:348-354, 1992; Ibba, Biotechnol. Genet. Eng. 13:197-216, 1995, Cahillet al., Trends Biochem. Sci., 14:400-403, 1989; Benner, Trends.Biotechnol., 12:158-163, 1994) all of which are herein incorporated byreference at least for material related to amino acid analogs).

Molecules can be produced that resemble peptides, but which are notconnected via a natural peptide linkage. For example, linkages for aminoacids or amino acid analogs can include CH₂NH—, —CH₂S—, —CH₂—CH₂—,—CH═CH—(cis and trans), —COCH₂—, —CH(OH)CH₂—, and —CHH₂SO— (These andothers can be found in Spatola, A. F. in Chemistry and Biochemistry ofAmino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker,New York, p. 267, 1983; Spatola, A. F., Vega Data (March 1983), Vol. 1,Issue 3, Peptide Backbone Modifications (general review); Morley, TrendsPharm. Sci. 463-468, 1980; Hudson, D. et al., Int. J. Pept. Prot. Res.14:177-185, 1979 (—CH₂NH—, CH₂CH₂—); Spatola et al. Life Sci.38:1243-1249, 1986 (—CHH₂—S); Hann J. Chem. Soc. Perkin Trans. 1307-314,1982 (—CH—CH—, cis and trans); Almquist et al. J. Med. Chem.23:1392-1398, 1980 (—COCH₂—); Jennings-White et al. Tetrahedron Lett.,23:2533, 1982 (—COCH₂—); Szelke et al. European Appln., EP 45665 CA:97:39405, 1982 (—CH(OH)CH₂—); Holladay et al. Tetrahedron Lett.24:4401-4404, 1983 (—C(OH)CH₂—); and Hruby Life Sci. 31:189-199, 1982(—CH₂—S—); each of which is incorporated herein by reference. Aparticularly preferred non-peptide linkage is —CH₂NH—. It is understoodthat peptide analogs can have more than one atom between the bond atoms,such as b-alanine, g-aminobutyric acid, and the like.

Amino acid analogs and analogs and peptide analogs often have enhancedor desirable properties, such as, more economical production, greaterchemical stability, enhanced pharmacological properties (half-life,absorption, potency, efficacy, etc.), altered specificity (e.g., abroad-spectrum of biological activities), reduced antigenicity, andothers.

D-amino acids can be used to generate more stable peptides, because Damino acids are not recognized by peptidases and such. Systematicsubstitution of one or more amino acids of a consensus sequence with aD-amino acid of the same type (e.g., D-lysine in place of L-lysine) canbe used to generate more stable peptides. Cysteine residues can be usedto cyclize or attach two or more peptides together. This can bebeneficial to constrain peptides into particular conformations. (Rizoand Gierasch Ann. Rev. Biochem. 61:387, 1992, incorporated herein byreference).

6. Supplements

Also disclosed herein are nutritional supplements. A nutritionalsupplement is any compound or composition that can be administered to ortaken by a subject to provide, supply, or increase a nutrient(s) (e.g.,vitamin, mineral, essential trace element, amino acid, peptide, nucleicacid, oligonucleotide, lipid, cholesterol, steroid, carbohydrate, andthe like). In one aspect, disclosed herein are nutritional supplementscomprising any of the compounds disclosed herein. For example, anutritional supplement can comprise any of the lipids disclosed herein.The fatty acid residues of these lipids can be any fatty acid asdisclosed herein (e.g., unsaturated or saturated fatty acid residues).

The nutritional supplement can comprise any amount of the compoundsdisclosed herein, but will typically contain an amount determined tosupply a subject with a desired dose of a benzenediol derivative (e.g.,CoQ₁₀) and/or fatty acids. The exact amount of compound required in thenutritional supplement will vary from subject to subject, depending onthe species, age, weight and general condition of the subject, theseverity of the dietary deficiency being treated, the particular mode ofadministration, and the like. Thus, it is not possible to specify anexact amount for every nutritional supplement. However, an appropriateamount can be determined by one of ordinary skill in the art using onlyroutine experimentation given the teachings herein. In one specificexample, a nutritional supplement can comprise from about 0.05 to about20%, from about 1 to about 7.5%, or from about 3 to about 5% by weightof the compound. In another example, the nutritional supplement cancomprise from about 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40,0.45, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.0,1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0,8.5, 9.0, 9.5, 10, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5,15.0, 15.5, 16.0, 16.5, 17.0, 17.5, 18.0, 18.5, 19.0, 19.5, or 20.0% byweight of the compound, where any of the stated values can form an upperor lower endpoint when appropriate. In another aspect, when thenutritional supplement, the supplement can be composed of up to 100% ofthe supplement.

The nutritional supplement can also comprise other nutrient(s) such asvitamins trace elements, minerals, and the like. Further, thenutritional supplement can comprise other components such aspreservatives, antimicrobials, anti-oxidants, chelating agents,thickeners, flavorings, diluents, emulsifiers, dispersing aids, and/orbinders.

The nutritional supplements are generally taken orally and can be in anyform suitable for oral administration. For example, a nutritionalsupplement can typically be in a tablet, gel-cap, capsule, liquid,sachets, or syrup form.

7. Delivery Devices

Any of the compounds described herein can be incorporated into adelivery device. Examples of delivery devices include, but are notlimited to, microcapsules, microspheres, nanospheres or nanoparticles,liposomes, noisome, nanoerythrosome, solid-liquid nanoparticles, gels,gel capsules, tablets, lotions, creams, sprays, or emulsions. Otherexamples of delivery devices that are suitable for non-oraladministration include pulmospheres. Examples of particular deliverydevices useful herein are described below.

The disclosed compounds can be incorporated into liposomes. As is knownin the art, liposomes are generally derived from phospholipids or otherlipid substances. Liposomes are formed by mono- or multi-lamellarhydrated liquid crystals that are dispersed in an aqueous medium. Anynon-toxic, physiologically acceptable and metabolizable lipid capable offorming liposomes can be used. The disclosed compositions in liposomeform can contain, in addition to a compound disclosed herein,stabilizers, preservatives, excipients, and the like. Examples ofsuitable lipids are the phospholipids and the phosphatidylcholines(lecithins), both natural and synthetic. Methods of forming liposomesare known in the art. See, e.g., Prescott, Ed., Methods in Cell Biology,Volume XIV, Academic Press, New York, p. 33 et seq., 1976, which ishereby incorporated by reference herein for its teachings of liposomesand their preparation.

In other examples, the liposomes can be cationic liposomes (e.g., DOTMA,DOPE, DC cholesterol) or anionic liposomes. Liposomes can furthercomprise proteins to facilitate targeting a particular cell, if desired.Administration of a composition comprising a compound and a cationicliposome can be administered to the blood afferent to a target organ orinhaled into the respiratory tract to target cells of the respiratorytract. Regarding liposomes, see e.g., Brigham, et al., Am J Resp CellMol Biol 1:95-100, 1989; Felgner, et al., Proc Natl Acad Sci USA84:7413-7, 1987; and U.S. Pat. No. 4,897,355, which are incorporated byreference herein for their teachings of liposomes. As one example,delivery can be via a liposome using commercially available liposomepreparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc.,Gaithersburg, Md.), SUPERFECT (Qiagen, Inc. Hilden, Germany) andTRANSFECTAM (Promega Biotec, Inc., Madison, Wis.), as well as otherliposomes developed according to procedures standard in the art.Liposomes where the diffusion of the compound or delivery of thecompound from the liposome is designed for a specific rate or dosage canalso be used.

As described herein, noisomes are delivery devices that can be used todeliver the compositions disclosed herein. Noisomes are multilamellar orunilamellar vesicles involving non-ionic surfactants. An aqueoussolution of solute is enclosed by a bilayer resulting from theorganization of surfactant macromolecules. Similar to liposomes,noisomes are used in targeted delivery of, for example, anticancerdrugs, including methotrexate, doxorubicin, and immunoadjuvants. Theyare generally understood to be different from transferosomes, vesiclesprepared from amphiphilic carbohydrate and amino group containingpolymers, e.g., chitosan.

As described herein, nanoerythrosomes are delivery devices that can beused to deliver the compositions disclosed herein. Nanoerythrosomes arenano-vesicles made of red blood cells via dialysis through filters ofdefined pore size. These vesicles can be loaded with a diverse array ofbiologically active molecules, including proteins and the compositionsdisclosed herein. They generally serve as ideal carriers forantineoplastic agents like bleomycin, actinomycin D, but can be used forsteroids, other lipids, etc.

Artificial red blood cells, as described herein, are further deliverydevices that can be used to deliver the compositions disclosed herein.Artificial red blood cells can be generated by interfacialpolymerization and complex emulsion methods. Generally, the “cell” wallis made of polyphtaloyl L-lysine polymer/polystyrene and the core ismade of a hemoglobin solution from sheep hemolysate. Hemoglobin loadedmicrospheres typically have particle sizes of from about 1 to about 10mm. Their size, flexibility, and oxygen carrying capacity is similar tored blood cells.

Solid-lipid nanoparticles, as described herein, are other deliverydevices that can be used to deliver the compositions disclosed herein.Solid-lipid nanoparticles are nanoparticles, which are dispersed in anaqueous surfactant solution. They are comprised of a solid hydrophobiccore having a monolayer of a phospholipid coating and are usuallyprepared by high-pressure homogenization techniques. Immunomodulatingcomplexes (ISCOMS) are examples of solid-lipid nanoparticles. They arecage-like 40 nm supramolecular assemblies comprising of phospholipid,cholesterol, and hydrophobic antigens and are used mostly asimmunoadjuvants. For instance, ISCOMs are used to prolong blood-plasmalevels of subcutaneously injected cyclosporine.

Microspheres and micro-capsules, as described herein, are yet otherdelivery devices that can be used to deliver the compositions disclosedherein. In contrast to liposomal delivery systems, microspheres andmicro-capsules typically do not have an aqueous core but a solid polymermatrix or membrane. These delivery devices are obtained by controlledprecipitation of polymers, chemical cross-linking of soluble polymers,and interfacial polymerization of two monomers or high-pressurehomogenization techniques. The encapsulated compound is graduallyreleased from the depot by erosion or diffusion from the particles.Successful formulations of short acting peptides, such as LHRH agonistslike leuprorelin and triptoreline, have been developed. Poly(lactideco-glycolide (PLGA) microspheres are currently used as monthly and threemonthly dosage forms in the treatment of advanced prostrate cancer,endometriosis, and other hormone responsive conditions. Leuprolide, anLHRH superagonist, was incorporated into a variety of PLGA matricesusing a solvent extraction/evaporation method. As noted, all of thesedelivery devices can be used in the methods disclosed herein.

Pulmospheres are still other examples of delivery devices that can beused herein. Pulmospheres are hollow porous particles with a low density(less than about 0.1 m mL⁻¹). Pulmospheres typically have excellentre-dispersibility and are usually prepared by supercritical fluidcondensation technology. Co-spray-drying with certain matrices, such ascarbohydrates, human serum albumin, etc., can improve the stability ofproteins and peptides (e.g., insulin) and other biomolecules forpulmonary delivery. This type of delivery could be also accomplishedwith micro-emulsions and lipid emulsions, which are ultra fine, thin,transparent oil-in-water (o/w) emulsions formed spontaneously with nosignificant input of mechanical energy. In this technique, an emulsioncan be prepared at a temperature, which must be higher than the phaseinversion temperature of the system. At elevated temperature theemulsion is of water-in-oil (w/o) type and as it cools at the phaseinversion temperature, this emulsion is inverted to become o/w. Due totheir very small inner phase, they are extremely stable and used forsustained release of steroids and vaccines. Lipid emulsions comprise aneutral lipid core (i.e., triglycerides) stabilized by a monolayer ofamphiphilic lipid (i.e., phospholipid) using surfactants like egglecithin triglycerides and miglyol. They are suitable for passive andactive targeting.

There are other oral delivery systems under investigation that are basedon osmotic pressure modulation, pH modulation, swelling modulation,altered density and floating systems, mucoadhesiveness etc. Theseformulations and time-delayed formulations to deliver drugs inaccordance with circadian rhythm of disease that are currently in use orinvestigation can be applied for delivery of the compositions disclosedherein.

In one particular aspect disclosed herein, the disclosed compounds,including nutritional supplement and pharmaceutical formulationsthereof, can be incorporated into microcapsules as described herein.

In one aspect disclosed herein, the disclosed compounds can beincorporated into microcapsules. In one aspect, the microcapsulecomprises an agglomeration of primary microcapsules and the chromiumcompounds described herein, each individual primary microcapsule havinga primary shell, wherein the chromium compound is encapsulated by theprimary shell, wherein the agglomeration is encapsulated by an outershell. These microcapsules are referred to herein as “multicoremicrocapsules.”

In another aspect, described herein are microcapsules comprising achromium compound, a primary shell, and a secondary shell, wherein theprimary shell encapsulates the chromium compound, and the secondaryshell encapsulates the loading substance and primary shell. Thesemicrocapsules are referred to herein as “single-core microcapsules.

Optionally, other loading substances can be encapsulated with thechromium compound. The loading substance can be any substance that isnot entirely soluble in the aqueous mixture. In one aspect, the loadingsubstance is a solid, a hydrophobic liquid, or a mixture of a solid anda hydrophobic liquid. In another aspect, the loading substance comprisesa grease, an oil, a lipid, a drug (e.g., small molecule), a biologicallyactive substance, a nutritional supplement (e.g., vitamins), a flavorcompound, or a mixture thereof. Examples of oils include, but are notlimited to, animal oils (e.g., fish oil, marine mammal oil, etc.),vegetable oils (e.g., canola or rapeseed), mineral oils, derivativesthereof or mixtures thereof. The loading substance can be a purified orpartially purified oily substance such as a fatty acid, a triglycerideor ester thereof, or a mixture thereof. In another aspect, the loadingsubstance can be a carotenoid (e.g., lycopene), a satiety agent, aflavor compound, a drug (e.g., a water insoluble drug), a particulate,an agricultural chemical (e.g., herbicides, insecticides, fertilizers),or an aquaculture ingredient (e.g., feed, pigment).

In one aspect, the loading substance can be an omega-3 fatty acid.Examples of omega-3 fatty acids include, but are not limited to,a-linolenic acid (18:3n3), octadecatetraenoic acid (18:4n3),eicosapentaenoic acid (20:5n3) (EPA), docosahexaenoic acid (22:6n3)(DHA), docosapentaenoic acid (22:5n3) (DPA), eicosatetraenoic acid(20:4n3), uncosapentaenoic acid (21:5n3), docosapentaenoic acid (22:5n3)and derivatives thereof and mixtures thereof. Many types of derivativesof omega-3 fatty acids are well known in the art. Examples of suitablederivatives include, but are not limited to, esters, such as phytosterolesters, branched or unbranched C₁-C₃₀ alkyl esters, branched orunbranched C₂-C₃₀ alkenyl esters, or branched or unbranched C₃-C₃₀cycloalkyl esters such as phytosterol esters and C₁-C₆ alkyl esters.Sources of oils can be derived from aquatic organisms (e.g., anchovies,capelin, Atlantic cod, Atlantic herring, Atlantic mackerel, Atlanticmenhaden, salmonids, sardines, shark, tuna, etc) and plants (e.g., flax,vegetables, etc) and microorganisms (e.g., fungi and algae).

In one aspect, the loading substance can contain an antioxidant.Examples of antioxidants include, but are not limited to, vitamin E,CoQ₁₀, tocopherols, lipid soluble derivatives of more polar antioxidantssuch as ascorbyl fatty acid esters (e.g., ascorbyl palmitate), plantextracts (e.g., rosemary, sage and oregano oils), algal extracts, andsynthetic antioxidants (e.g., BHT, TBHQ, ethoxyquin, alkyl gallates,hydroquinones, tocotrienols).

A number of different polymers can be used to produce the shell layersof the single and multicore microcapsules. Examples of such polymersinclude, but are not limited to, a protein, a polyphosphate, apolysaccharide, or a mixture thereof. In another aspect, the shellmaterial used to prepare the single- and multicore microcapsules furthercomprises In another aspect, the shell material used to prepare thesingle- and multicore microcapsules further comprises gelatin type A,gelatin type B, polyphosphate, gum arabic, alginate, chitosan,carrageenan, pectin, starch, modified starch, alfa-lactalbumin,beta-lactoglobumin, ovalbumin, polysorbiton, maltodextrins,cyclodextrins, cellulose, methyl cellulose, ethyl cellulose,hydropropylmethylcellulose, carboxymethylcellulose, milk protein, wheyprotein, soy protein, canola protein, albumin, chitin, polylactides,poly-lactide-co-glycolides, derivatized chitin, chitosan, poly-lysine,various inorganic-organic composites, or any mixture thereof. It is alsocontemplated that derivatives of these polymers can be used as well. Inanother aspect, the polymer can be kosher gelatin, non-kosher gelatin,Halal gelatin, or non-Halal gelatin.

In one aspect, one or more of the shell layers in the single andmulticore microcapsules comprises gelatin having a Bloom number lessthan 50. This gelatin is referred to herein as “low Bloom gelatin.” TheBloom number describes the gel strength formed at 10° C. with a 6.67%solution gelled for 18 hours. In one aspect, the low Bloom gelatin has aBloom number less than 40, less than 30, less than 20, or less than 10.In another aspect, the gelatin has a Bloom number of 45, 40, 35, 30, 25,20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0, where any two values can beused to produce a range. In another aspect, the low Bloom gelatin is inboth the primary shell and the outer shell of the multicoremicrocapsule. In one aspect, the low Bloom gelatin is gelatin type A. Inanother aspect, the low Bloom gelatin is gelatin type A produced byKenney & Ross Ltd., R.R. #3 Shelburne, NS Canada. In another aspect,gelatin having a Bloom number of zero is in both the primary shell andthe outer shell of the multicore microcapsule.

In one aspect, the material used to make the shells of the single- ormulticore microcapsules is a two-component system made from a mixture oftwo different types of polymers. In one aspect, the material is acomplex coacervate between the polymer components. Complex coacervationis caused by the interaction between two oppositely charged polymers. Inone aspect, the shell material used to produce the single and multicoremicrocapsules is composed of (1) low Bloom gelatin and (2) gelatin typeB, polyphosphate, gum arabic, alginate, chitosan, carrageenan, pectin,carboxymethylcellulose, whey protein, soy protein, canola protein,albumin, or a mixture thereof. The molar ratio of the different polymerscan vary. For example, the molar ratio of low Bloom gelatin to the otherpolymer component is from 1:5 to 15:1. For example, when low Bloomgelatin and polyphosphate are used, the molar ratio of low Bloom gelatinto polyphosphate is about 8:1 to about 12:1; when low Bloom gelatin andgelatin type B are used, the molar ratio is 2:1 to 1:2; and when lowBloom gelatin and alginate are used, the molar ratio is 3:1 to 8:1.

Processing aids can be included in the shell material (e.g., primary orouter shells). Processing aids can be used for a variety of reasons. Forexample, they may be used to promote agglomeration of the primarymicrocapsules, stabilize the emulsion system, improve the properties ofthe outer shells, control microcapsule size and/or to act as anantioxidant. In one aspect, the processing aid can be an emulsifier, afatty acid, a lipid, a wax, a microbial cell (e.g., yeast cell lines), aclay, or an inorganic compound (e.g., calcium carbonate). Not wishing tobe bound by theory, these processing aids can improve the barrierproperties of the microcapsules. In one aspect, one or more antioxidantscan be added to the shell material. Antioxidant properties are usefulboth during the process (e.g. during coacervation and/or spray drying)and in the microcapsules after they are formed (i.e. to extendshelf-life, etc). Preferably a small number of processing aids thatperform a large number of functions can be used. In one aspect, theantioxidant can be a phenolic compound, a plant extract, or asulphur-containing amino acid. In one aspect, ascorbic acid (or a saltthereof such as sodium or potassium ascorbate) can be used to promoteagglomeration of the primary microcapsules, to control microcapsule sizeand to act as an antioxidant. The antioxidant can be used in an amountof about 100 ppm to about 12,000 ppm, or from about 1,000 ppm to about5,000 ppm. Other processing aids such as, for example, metal chelators,can be used as well. For example, ethylene diamine tetraacetic acid canbe used to bind metal ions, which can reduce the catalytic oxidation ofthe loading substance.

In one aspect, the primary microcapsules (primary shells) have anaverage diameter of about 40 nm to about 10 μm, 0.1 μm to about 10 μm, 1μm to about 10 μm, 1 μm to about 8 μm, 1 μm to about 6 μm, 1 μm to about4 μm, or 1 μm to about 2 μm, or 1 μm. In another aspect, the multicoremicrocapsules can have an average diameter of from about 1 μm to about2000 μm, 20 μm to about 1000 μm, from about 20 μm to about 100 μm, orfrom about 30 μm to about 80 μm. In another aspect, the single-coremicrocapsules have an outer diameter of from 1 μm to 2,000 μm.

The microcapsules described herein generally have a combination of highpayload and structural strength. For example, payloads of loadingsubstance can be from 20% to 90%, 50% to 70% by weight, or 60% by weightof the single or multicore microcapsules.

In one aspect, the methods disclosed in U.S. Patent ApplicationPublication No. 2003/0193102, which is incorporated by reference in itsentirety, can be used to encapsulate the chromium compounds describedherein. It is also contemplated that one or more additional shell layerscan be placed on the outer shell of the single or multicoremicrocapsules. In one aspect, the techniques described in InternationalPublication No. WO 2004/041251 A1, which is incorporated by reference inits entirety, can be used to add additional shell layers to the singleand multicore microcapsules.

a) Pharmaceutical and Nutraceutical Compositions

These lipids and antioxidants are targeted for use in animal feeds,pharmaceuticals, nutraceuticals (especially infant formula) as well asin the industry. This is to also include nutraceutical forms of deliverysuch as gel capsules and the like, common microencapsulations, etc.

As described above, the compositions can also be administered in vivo ina pharmaceutically acceptable carrier. By “pharmaceutically acceptable”is meant a material that is not biologically or otherwise undesirable,i.e., the material may be administered to a subject, along with thenucleic acid or vector, without causing any undesirable biologicaleffects or interacting in a deleterious manner with any of the othercomponents of the pharmaceutical composition in which it is contained.The carrier would naturally be selected to minimize any degradation ofthe active ingredient and to minimize any adverse side effects in thesubject, as would be well known to one of skill in the art.

The compositions may be administered orally, parenterally (e.g.,intravenously), by intramuscular injection, by intraperitonealinjection, transdermally, extracorporeally, topically or the like,including topical intranasal administration or administration byinhalant. As used herein, “topical intranasal administration” meansdelivery of the compositions into the nose and nasal passages throughone or both of the nares and can comprise delivery by a sprayingmechanism or droplet mechanism, or through aerosolization of the nucleicacid or vector. Administration of the compositions by inhalant can bethrough the nose or mouth via delivery by a spraying or dropletmechanism. Delivery can also be directly to any area of the respiratorysystem (e.g., lungs) via intubation. The exact amount of thecompositions required will vary from subject to subject, depending onthe species, age, weight and general condition of the subject, theseverity of the allergic disorder being treated, the particular nucleicacid or vector used, its mode of administration and the like. Thus, itis not possible to specify an exact amount for every composition.However, an appropriate amount can be determined by one of ordinaryskill in the art using only routine experimentation given the teachingsherein.

Parental administration of the composition, if used, is generallycharacterized by injection. Injectables can be prepared in conventionalforms, either as liquid solutions or suspensions, solid forms suitablefor solution of suspension in liquid prior to injection, or asemulsions. A more recently revised approach for parenteraladministration involves use of a slow release or sustained releasesystem such that a constant dosage is maintained. See, e.g., U.S. Pat.No. 3,610,795, which is incorporated by reference herein.

The materials may be in solution, suspension (for example, incorporatedinto microparticles, liposomes, or cells). These may be targeted to aparticular cell type via antibodies, receptors, or receptor ligands. Thefollowing references are examples of the use of this technology totarget specific proteins to tumor tissue (Senter, et al., BioconjugateChem., 2:447-451, 1991; Bagshawe, K. D., Br. J. Cancer, 60:275-281,1989; Bagshawe, et al., Br. J. Cancer, 58:700-703, 1988; Senter, et al.,Bioconjugate Chem., 4:3-9, 1993; Battelli, et al., Cancer Immunol.Immunother., 35:421-425, 1992; Pietersz and McKenzie, Immunolog.Reviews, 129:57-80, 1992; and Roffler, et al., Biochem. Pharmacol.,42:2062-2065, 1991). Vehicles such as “stealth” and other antibodyconjugated liposomes (including lipid mediated drug targeting to coloniccarcinoma), receptor mediated targeting of DNA through cell specificligands, lymphocyte directed tumor targeting, and highly specifictherapeutic retroviral targeting of murine glicoma cells in vivo. Thefollowing references are examples of the use of this technology totarget specific proteins to tumor tissue (Hughes et al., CancerResearch, 49:6214-6220, 1989); and Litzinger and Huang, Biochimica etBiophysica Acta, 1104:179-187, 1992). In general, receptors are involvedin pathways of endocytosis, either constitutive or ligand induced. Thesereceptors cluster in clathrin-coated pits, enter the cell viaclathrin-coated vesicles, pass through an acidified endosome in whichthe receptors are sorted, and then either recycle to the cell surface,become stored intracellularly, or are degraded in lysosomes. Theinternalization pathways serve a variety of functions, such as nutrientuptake, removal of activated proteins, clearance of macromolecules,opportunistic entry of viruses and toxins, dissociation and degradationof ligand, and receptor-level regulation. Many receptors follow morethan one intracellular pathway, depending on the cell type, receptorconcentration, type of ligand, ligand valency, and ligand concentration.Molecular and cellular mechanisms of receptor-mediated endocytosis hasbeen reviewed (Brown and Greene, DNA and Cell Biology 10:399-409, 1991).

(1) Pharmaceutically Acceptable Carriers

The compositions, including antibodies, can be used therapeutically incombination with a pharmaceutically acceptable carrier.

Suitable carriers and their formulations are described in Remington: TheScience and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, MackPublishing Company, Easton, Pa. 1995. Typically, an appropriate amountof a pharmaceutically-acceptable salt is used in the formulation torender the formulation isotonic. Examples of thepharmaceutically-acceptable carrier include, but are not limited to,saline, Ringer's solution and dextrose solution. The pH of the solutionis preferably from about 5 to about 8, and more preferably from about 7to about 7.5. Further carriers include sustained release preparationssuch as semipermeable matrices of solid hydrophobic polymers containingthe antibody, which matrices are in the form of shaped articles, e.g.,films, liposomes or microparticles. It will be apparent to those personsskilled in the art that certain carriers may be more preferabledepending upon, for instance, the route of administration andconcentration of composition being administered.

Pharmaceutical carriers are known to those skilled in the art. Thesemost typically would be standard carriers for administration of drugs tohumans, including solutions such as sterile water, saline, and bufferedsolutions at physiological pH. The compositions can be administeredintramuscularly or subcutaneously. Other compounds will be administeredaccording to standard procedures used by those skilled in the art.

Pharmaceutical compositions may include carriers, thickeners, diluents,buffers, preservatives, surface active agents and the like in additionto the molecule of choice. Pharmaceutical compositions may also includeone or more active ingredients such as antimicrobial agents,anti-inflammatory agents, anesthetics, and the like.

The pharmaceutical composition may be administered in a number of waysdepending on whether local or systemic treatment is desired, and on thearea to be treated. Administration may be topically (includingophthalmically, vaginally, rectally, intranasally), orally, byinhalation, or parenterally, for example by intravenous drip,subcutaneous, intraperitoneal or intramuscular injection. The disclosedantibodies can be administered intravenously, intraperitoneally,intramuscularly, subcutaneously, intracavity, or transdermally.

Preparations for parenteral administration include sterile aqueous ornon-aqueous solutions, suspensions, and emulsions. Examples ofnon-aqueous solvents are propylene glycol, polyethylene glycol,vegetable oils such as olive oil, and injectable organic esters such asethyl oleate. Aqueous carriers include water, alcoholic/aqueoussolutions, emulsions or suspensions, including saline and bufferedmedia. Parenteral vehicles include sodium chloride solution, Ringer'sdextrose, dextrose and sodium chloride, lactated Ringer's, or fixedoils. Intravenous vehicles include fluid and nutrient replenishers,electrolyte replenishers (such as those based on Ringer's dextrose), andthe like. Preservatives and other additives may also be present such as,for example, antimicrobials, antioxidants, chelating agents, and inertgases and the like.

Formulations for topical administration may include ointments, lotions,creams, gels, drops, suppositories, sprays, liquids and powders.Conventional pharmaceutical carriers, aqueous, powder or oily bases,thickeners and the like may be necessary or desirable.

Compositions for oral administration include powders or granules,suspensions or solutions in water or non-aqueous media, capsules,sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers,dispersing aids or binders may be desirable.

Some of the compositions may potentially be administered as apharmaceutically acceptable acid- or base-addition salt, formed byreaction with inorganic acids such as hydrochloric acid, hydrobromicacid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, andphosphoric acid, and organic acids such as formic acid, acetic acid,propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid,malonic acid, succinic acid, maleic acid, and fumaric acid, or byreaction with an inorganic base such as sodium hydroxide, ammoniumhydroxide, potassium hydroxide, and organic bases such as mono-, di-,trialkyl and aryl amines and substituted ethanolamines.

(2) Therapeutic Uses

Effective dosages and schedules for administering the compositions maybe determined empirically, and making such determinations is within theskill in the art. The dosage ranges for the administration of thecompositions are those large enough to produce the desired effect inwhich the symptoms disorder are effected. The dosage should not be solarge as to cause adverse side effects, such as unwantedcross-reactions, anaphylactic reactions, and the like. Generally, thedosage will vary with the age, condition, sex and extent of the diseasein the patient, route of administration, or whether other drugs areincluded in the regimen, and can be determined by one of skill in theart. The dosage can be adjusted by the individual physician in the eventof any counterindications. Dosage can vary, and can be administered inone or more dose administrations daily, for one or several days.Guidance can be found in the literature for appropriate dosages forgiven classes of pharmaceutical products. For example, guidance inselecting appropriate doses for antibodies can be found in theliterature on therapeutic uses of antibodies, e.g., Handbook ofMonoclonal Antibodies, Ferrone et al., eds., Noges Publications, ParkRidge, N.J., (1985) ch. 22 and pp. 303-357; Smith et al., Antibodies inHuman Diagnosis and Therapy, Haber et al., eds., Raven Press, New York(1977) pp. 365-389. A typical daily dosage of the antibody used alonemight range from about 1 μg/kg to up to 100 mg/kg of body weight or moreper day, depending on the factors mentioned above.

b) Targeted Delivery

The disclosed liposomes and microcapsules can be targeted to aparticular cell type, such as islets cells, via antibodies, receptors,or receptor ligands. The following references are examples of the use ofthis technology to target specific tissue (Senter, et al., BioconjugateChem 2:447-51, 1991; Bagshawe, Br J Cancer 60:275-81, 1989; Bagshawe, etal., Br J Cancer 58:700-3, 1988; Senter, et al., Bioconjugate Chem4:3-9, 1993; Battelli, et al., Cancer Immunol Immunother 35:421-5, 1992;Pietersz and McKenzie, Immunolog Reviews 129:57-80, 1992; and Roffler,et al., Biochem Pharmacol 42:2062-5, 1991). These techniques can be usedfor a variety of other specific cell types.

8. Foodstuffs

Also disclosed herein are foodstuffs comprising any of the microcapsulesand emulsions disclosed herein. By “foodstuff” is meant any article thatcan be consumed (e.g., eaten, drank, or ingested) by a subject. In oneaspect, the microcapsules can be used as nutritional supplements to afoodstuff. For example, the microcapsules and emulsions can be loadedwith vitamins, omega-3 fatty acids, and other compounds that providehealth benefits. In one aspect, the foodstuff is a baked good, a pasta,a meat product, a frozen dairy product, a milk product, a cheeseproduct, an egg product, a condiment, a soup mix, a snack food, a nutproduct, a plant protein product, a hard candy, a soft candy, a poultryproduct, a processed fruit juice, a granulated sugar (e.g., white orbrown), a sauce, a gravy, a syrup, a nutritional bar, a beverage, a drybeverage powder, a jam or jelly, a fish product, or pet companion food.In another aspect, the foodstuff is bread, tortillas, cereal, sausage,chicken, ice cream, yogurt, milk, salad dressing, rice bran, fruitjuice, a dry beverage powder, rolls, cookies, crackers, snack food,fruit pies, or cakes.

9. Chips and Microarrays

Disclosed are chips where at least one address is the sequences or partof the sequences set forth in any of the nucleic acid sequencesdisclosed herein. Also disclosed are chips where at least one address isthe sequences or portion of sequences set forth in any of the peptidesequences disclosed herein.

Also disclosed are chips where at least one address is a variant of thesequences or part of the sequences set forth in any of the nucleic acidsequences disclosed herein. Also disclosed are chips where at least oneaddress is a variant of the sequences or portion of sequences set forthin any of the peptide sequences disclosed herein.

10. Computer Readable Mediums

It is understood that the disclosed nucleic acids and proteins can berepresented as a sequence consisting of the nucleotides of amino acids.There are a variety of ways to display these sequences, for example thenucleotide guanosine can be represented by G or g. Likewise the aminoacid valine can be represented by Val or V. Those of skill in the artunderstand how to display and express any nucleic acid or proteinsequence in any of the variety of ways that exist, each of which isconsidered herein disclosed. Specifically contemplated herein is thedisplay of these sequences on computer readable mediums, such as,commercially available floppy disks, tapes, chips, hard drives, compactdisks, and video disks, or other computer readable mediums. Alsodisclosed are the binary code representations of the disclosedsequences. Those of skill in the art understand what computer readablemediums. Thus, computer readable mediums on which the nucleic acids orprotein sequences are recorded, stored, or saved.

Disclosed are computer readable mediums comprising the sequences andinformation regarding the sequences set forth herein.

11. Kits

Disclosed herein are kits that are drawn to reagents that can be used inpracticing the methods disclosed herein or in using or keeping thecompositions disclosed herein. The kits can include any reagent orcombination of reagent discussed herein or that would be understood tobe required or beneficial in the practice of the disclosed methods. Forexample, the kits could include one or more of the eukaryoticmicroorganisms disclosed herein along with, for example, media for theirmaintenance. The kits could also include, for example, the lipids orantioxidants, along with means for using or administering these.

12. Compositions with Similar Functions

It is understood that the compositions disclosed herein have certainfunctions, such as producing certain ratios of lipids. Disclosed hereinare certain structural, genetic, and functional requirements forperforming the disclosed functions, and it is understood that there area variety of structures, genetic backgrounds, and functional backgroundswhich can perform the same function which are related to the disclosedstructures, and that these structures will ultimately achieve the sameresult, for example production of a certain ration of lipids.

D. METHODS OF MAKING THE COMPOSITIONS

The compositions disclosed herein and the compositions necessary toperform the disclosed methods can be made using any method known tothose of skill in the art for that particular reagent or compound unlessotherwise specifically noted.

1. Nucleic Acid Synthesis

For example, the nucleic acids, such as, the oligonucleotides to be usedas primers can be made using standard chemical synthesis methods or canbe produced using enzymatic methods or any other known method. Suchmethods can range from standard enzymatic digestion followed bynucleotide fragment isolation (see for example, Sambrook et al.,Molecular Cloning: A Laboratory Manual, 2nd Edition (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989) Chapters 5, 6) topurely synthetic methods, for example, by the cyanoethyl phosphoramiditemethod using a Milligen or Beckman System 1Plus DNA synthesizer (forexample, Model 8700 automated synthesizer of Milligen-Biosearch,Burlington, Mass. or ABI Model 380B). Synthetic methods useful formaking oligonucleotides are also described by Ikuta et al., Ann. Rev.Biochem. 53:323-356, 1984, (phosphotriester and phosphite triestermethods), and Narang et al., Methods Enzymol., 65:610-620, 1980,(phosphotriester method). Protein nucleic acid molecules can be madeusing known methods such as those described by Nielsen et al.,Bioconjug. Chem. 5:3-7, 1994.

2. Peptide Synthesis

One method of producing the disclosed proteins is to link two or morepeptides or polypeptides together by protein chemistry techniques. Forexample, peptides or polypeptides can be chemically synthesized usingcurrently available laboratory equipment using either Fmoc(9-fluorenylmethyloxycarbonyl) or Boc (tert-butyloxycarbonoyl)chemistry. (Applied Biosystems, Inc., Foster City, Calif.). One skilledin the art can readily appreciate that a peptide or polypeptidecorresponding to the disclosed proteins, for example, can be synthesizedby standard chemical reactions. For example, a peptide or polypeptidecan be synthesized and not cleaved from its synthesis resin whereas theother fragment of a peptide or protein can be synthesized andsubsequently cleaved from the resin, thereby exposing a terminal groupwhich is functionally blocked on the other fragment. By peptidecondensation reactions, these two fragments can be covalently joined viaa peptide bond at their carboxyl and amino termini, respectively, toform an antibody, or fragment thereof. (Grant G A (1992) SyntheticPeptides: A User Guide. W.H. Freeman and Co., N.Y. (1992); Bodansky Mand Trost B., Ed. (1993) Principles of Peptide Synthesis.Springer-Verlag Inc., NY (which is herein incorporated by reference atleast for material related to peptide synthesis). Alternatively, thepeptide or polypeptide is independently synthesized in vivo as describedherein. Once isolated, these independent peptides or polypeptides may belinked to form a peptide or fragment thereof via similar peptidecondensation reactions.

For example, enzymatic ligation of cloned or synthetic peptide segmentsallow relatively short peptide fragments to be joined to produce largerpeptide fragments, polypeptides or whole protein domains (Abrahmsen L etal., Biochemistry, 30:4151, 1991). Alternatively, native chemicalligation of synthetic peptides can be utilized to syntheticallyconstruct large peptides or polypeptides from shorter peptide fragments.This method consists of a two step chemical reaction (Dawson et al.Science, 266:776-779, 1994). The first step is the chemoselectivereaction of an unprotected synthetic peptide— thioester with anotherunprotected peptide segment containing an amino-terminal Cys residue togive a thioester-linked intermediate as the initial covalent product.Without a change in the reaction conditions, this intermediate undergoesspontaneous, rapid intramolecular reaction to form a native peptide bondat the ligation site (Baggiolini M et al. FEBS Lett. 307:97-101, 1992;Clark-Lewis I et al., J. Biol. Chem., 269:16075, 1994; Clark-Lewis I etal., Biochemistry, 30:3128, 1991; Rajarathnam K et al., Biochemistry33:6623-30, 1994).

Alternatively, unprotected peptide segments are chemically linked wherethe bond formed between the peptide segments as a result of the chemicalligation is an unnatural (non-peptide) bond (Schnolzer, M et al.Science, 256:221, 1992). This technique has been used to synthesizeanalogs of protein domains as well as large amounts of relatively pureproteins with full biological activity (de Lisle Milton R C et al.,Techniques in Protein Chemistry IV. Academic Press, New York, pp.257-267, 1992).

3. Processes for Making the Compositions

Disclosed are processes for making the compositions as well as makingthe intermediates leading to the compositions. For example, disclosedare eukaryotic microorganisms which can produce desired lipids andantioxidants as well as methods for isolating and purifying the desiredlipids and antioxidants. There are a variety of methods that can be usedfor making these compositions, such as synthetic chemical methods andstandard molecular biology methods. It is understood that the methods ofmaking these and the other disclosed compositions are specificallydisclosed.

Disclosed are cells produced by the process of transforming the cellwith any nucleic acid. Disclosed are cells produced by the process oftransforming the cell with any of the non-naturally occurring disclosednucleic acids.

Disclosed are any of the lipids produced by the disclosed eukaryoticmicroorganisms. Disclosed are any peptides produced by the process ofexpressing the peptide in the disclosed organisms. Methods of using thecompositions.

4. Methods of Using the Compositions as Research Tools

The disclosed compositions can be used in a variety of ways as researchtools and of the production of, for example, lipids and antioxidants.

The disclosed compositions can be used as discussed herein as eitherreagents in micro arrays or as reagents to probe or analyze existingmicroarrays. The disclosed compositions can be used in any known methodfor isolating or identifying single nucleotide polymorphisms. Thecompositions can also be used in any method for determining allelicanalysis of for example, the strains of the organisms disclosed herein,particularly allelic analysis as it relates to the production of lipidsand antioxidants. The compositions can also be used in any known methodof screening assays, related to chip/microarrays. The compositions canalso be used in any known way of using the computer readable embodimentsof the disclosed compositions, for example, to study relatedness or toperform molecular modeling analysis related to the disclosedcompositions.

5. Methods of Gene Modification and Gene Disruption

The disclosed compositions and methods can be used for targeted genedisruption and modification in any animal that can undergo these events.Gene modification and gene disruption refer to the methods, techniques,and compositions that surround the selective removal or alteration of agene or stretch of chromosome in an organism, such as the eukaryotesdisclosed herein, in a way that propagates the modification through thereplication of the organism. In general, for example, a cell istransformed with a vector which is designed to homologously recombinewith a region of a particular chromosome or nucleic acid containedwithin the cell, as for example, described herein. This homologousrecombination event can produce a chromosome which has exogenous DNAintroduced, for example in frame, with the surrounding DNA. This type ofprotocol allows for very specific mutations, such as point mutations, tobe introduced into the genome contained within the cell. Methods forperforming this type of homologous recombination are disclosed herein.

V. SPECIFIC EMBODIMENTS

Disclosed herein is a eukaryotic microorganism having an 18S sequence,wherein the 18S sequence has at least 94% identity to the sequence setforth in SEQ ID NO:1. The eukaryotic microorganism can produceunsaturated fatty acids having a profile shown in FIG. 2. The eukaryoticmicroorganism can be from the phylum Labyrinthulomycota, the classLabyrinthulomycetes, the subclass Thraustochytridae, the orderThraustochytriales, the family Thraustochytriaceae, and/or the genusThraustochytrium. The eukaryotic microorganism can be Thraustochytriumsp., Thraustochytrium aureum, Thraustochytrium roseum, orThraustochytrium striatum. The eukaryotic microorganism can also be fromthe family Thraustochytriaceae and can have ATCC accession number 20888,20889, 20890, 20891, or 20892.

Also disclosed herein is a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, wherein the microorganism is from thegenus Schizochytrium. The eukaryotic microorganism can be Schizochytriumsp.

Also disclosed herein is a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, wherein the eukaryotic microorganismcomprises an omega 3 or omega 6 fatty acid. The eukaryotic microorganismcan also comprises DHA or DPA.

Also disclosed herein is a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, wherein the microorganism produces alipid or fatty acid fraction of at least about 4 wt. % to 6 wt. %. Thelipid can comprise DHA. The lipid composition can also comprise fromabout 25 wt. % fatty acid fraction to about 40 wt. % fatty acid fractionof n-3 DHA, from about 6 wt. % fatty acid fraction to about 10 wt. %fatty acid fraction of n-6 DPA, and from about 0 wt. % fatty acidfraction to about 3 wt. % fatty acid fraction of n-3 EPA.

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1. The composition canfurther comprise a medium and/or nutrients

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1, wherein thecomposition is a biomass. The eukaryotic microorganism of thecomposition can be from the phylum Labyrinthulomycota, the classLabyrinthulomycetes, the subclass Thraustochytridae, the orderThraustochytriales, the family Thraustochytriaceae, or the genusThraustochytrium. The eukaryotic microorganism can be Thraustochytriumsp., Thraustochytrium aureum, Thraustochytrium roseum, orThraustochytrium striatum. The eukaryotic microorganism can also be fromthe family Thraustochytriaceae and can have ATCC accession number 20888,20889, 20890, 20891, or 20892.

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1, wherein themicroorganism is from the genus Schizochytrium. The eukaryoticmicroorganism can be Schizochytrium sp.

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1, wherein theeukaryotic microorganism produces unsaturated fatty acids having aprofile shown in FIG. 2. The unsaturated fatty acid can comprise anomega 3 or omega 6 fatty acid. The unsaturated fatty acid can alsocomprise DHA or DPA.

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1, wherein theeukaryotic microorganism can produce a lipid or fatty acid fraction ofat least about 4 wt. % to 6 wt. %. The lipid can comprise DHA. The lipidcan also comprise from about 25 wt. % fatty acid fraction to about 40wt. % fatty acid fraction of n-3 DHA, from about 6 wt. % fatty acidfraction to about 10 wt. % fatty acid fraction of n-6 DPA, and fromabout 0 wt. % fatty acid fraction to about 3 wt. % fatty acid fractionof n-3 EPA.

Also disclosed is a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 80%identity to the sequence set forth in SEQ ID NO:1

Also disclosed is a comprising from about 25 wt. % fatty acid fractionto about 40 wt. % fatty acid fraction of n-3 DHA, from about 6 wt. %fatty acid fraction to about 10 wt. % fatty acid fraction of n-6 DPA,and from about 0 wt. % fatty acid fraction to about 3 wt. % fatty acidfraction of n-3 EPA.

Also disclosed is a method of preparing a lipid composition, the methodcomprising: culturing the eukaryotic microorganism described herein, ina heterotrophic medium, and isolating the lipid composition. Alsodisclosed is a lipid composition prepared according to this method.

Also disclosed is a delivery device comprising a any of the compositionsdescribed above. For example, disclosed is a delivery device comprisinga composition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1. The delivery device can comprise amicrocapsule, a microsphere, a nanosphere or nanoparticle, a liposome, anoisome, a nanoerythrosome, a solid-liquid nanoparticle, a leuprolide, agel, a gel capsule, a tablet, a lotion, a cream, a spray, an emulsion,or a powder.

Also disclosed is a microcapsule, comprising an agglomeration of primarymicrocapsules and a loading substance, each individual primarymicrocapsule having a primary shell, wherein the loading substancecomprises any of the compositions described above, and is encapsulatedby the primary shell, and wherein the agglomeration is encapsulated byan outer shell. The primary shell and/or outer shell can comprise asurfactant, gelatin, polyphosphate, polysaccharide, or a mixturethereof. The primary shell and/or outer shell can also comprise gelatintype B, polyphosphate, gum arabic, alginate, chitosan, carrageenan,pectin, starch, modified starch, alfa-lactalbumin, beta-lactoglobumin,ovalbumin, polysorbiton, maltodextrin, cyclodextrin, cellulose, methylcellulose, ethyl cellulose, hydropropylmethylcellulose,carboxymethylcellulose, milk protein, whey protein, soy protein, canolaprotein, albumin, kosher gelatin, non-kosher gelatin, Halal gelatin,non-Halal gelatin, or a mixture thereof. The primary shell and/or outershell can also comprise a complex coacervate, gelatin type A, fishgelatin, a gelatin with a Bloom number of from about 0 to about 300, agelatin with a Bloom number of from about 0 to about 50, a gelatin witha Bloom number of from about 51 to about 300, a gelatin with a Bloomnumber of about 0, about 210, about 220, or about 240, a coacervate ofgelatin and polyphosphate.

The loading substance of the disclosed microcapsules can comprise oilfrom Thraustochytrium, Schizochytrium, or a mixture thereof. The loadingsubstance can be from about 20% to about 90% or 50% to about 70% byweight of the microcapsule.

The outer shell of the disclosed microcapsules can have an averagediameter of from about 1 μm to about 2,000 μm, about 20 μm to about1,000 μm, about 30 μm to about 80 μm, about 40 nm to about 10 μm, orabout 0.1 μm to about 5 μm.

Also disclosed is a nutritional supplement that comprises any of thecompositions, delivery devices, or microcapsules described above. Thedisclosed nutritional supplements can be in the form of a tablet,gel-cap, capsule, liquid, or syrup.

Also disclosed is a foodstuff that comprises any of the compositions,delivery devices, or microcapsules described above. The foodstuff can bea baked good, a pasta, a meat product, a frozen dairy product, a milkproduct, a cheese product, an egg product, a condiment, a soup mix, asnack food, a nut product, a plant protein product, a hard candy, a softcandy, a poultry product, a processed fruit juice, a granulated sugar, asauce, a gravy, a syrup, a nutritional bar, a beverage, a dry beveragepowder, a jam or jelly, an infant formula, or a baby food. The foodstuffcan also be a fish product, a companion pet food, a livestock or anaquaculture feed. The foodstuff can also be bread, tortillas, cereal,sausage, chicken, ice cream, yogurt, milk, salad dressing, rice bran,fruit juice, a dry beverage powder, rolls, cookies, crackers, fruitpies, or cakes.

Also disclosed is a method of delivering a composition to a subject,comprising administering to the subject any of the compositions,delivery devices, microcapsules, or foodstuffs described above. Thesubject can be a mammal. The subject can also be a human.

Also disclosed is a use of any of the microcapsules described above andto prepare a medicament for delivering a loading substance to a subject.

Also disclosed is a method of lowering cholesterol levels, triglyceridelevels, or a combination thereof in a subject, comprising the step ofadministering to the subject an effective amount of any of thecompositions, delivery devices, microcapsules, nutritional supplements,or foodstuffs described above.

Also disclosed is a method of supplementing essential trace elements ina subject, the method comprising the step of administering to thesubject an effective amount of any of the compositions, deliverydevices, microcapsules, nutritional supplements, or foodstuffs describedabove, wherein the composition, delivery device, microcapsule,supplement, and foodstuff comprises an essential trace element.

Also disclosed is a method of improving insulin sensitivity in asubject, comprising the step of administering to the subject aneffective amount of any of the compositions, delivery devices,microcapsules, nutritional supplements, or foodstuffs described above.

Also disclosed is a method of reducing hyperglycemia in a subject,comprising the step of administering to the subject an effective amountof any of the compositions, delivery devices, microcapsules, nutritionalsupplements, or foodstuffs described above.

Also disclosed is a method of reducing hypercholesterolemia in asubject, comprising the step of administering to the subject aneffective amount of any of the compositions, delivery devices,microcapsules, nutritional supplements, or foodstuffs described above.

Also disclosed is a method of reducing body fat in a subject, comprisingthe step of administering to the subject an effective amount of any ofthe compositions, delivery devices, microcapsules, nutritionalsupplements, or foodstuffs described above.

Also disclosed is a method of promoting weight loss in a subject,comprising the step of administering to the subject an effective amountof any of the compositions, delivery devices, microcapsules, nutritionalsupplements, or foodstuffs described above.

Also disclosed is a method of treating or preventing diabetes in asubject, comprising the step of administering to the subject aneffective amount of any of the compositions, delivery devices,microcapsules, nutritional supplements, or foodstuffs described above.

Also disclosed is a pharmaceutical formulation comprising any of thecompositions, delivery devices, or microcapsules described above, and apharmaceutical carrier.

Also disclosed is a foodstuff comprising a composition comprising aeukaryotic microorganism having an 18S sequence, wherein the 18Ssequence has at least 94% identity to the sequence set forth in SEQ IDNO:1. The foodstuff can be a baked good, a pasta, a meat product, afrozen dairy product, a milk product, a cheese product, an egg product,a condiment, a soup mix, a snack food, a nut product, a plant proteinproduct, a hard candy, a soft candy, a poultry product, a processedfruit juice, a granulated sugar, a sauce, a gravy, a syrup, anutritional bar, a beverage, a dry beverage powder, a jam or jelly, aninfant formula, or a baby food. The foodstuff can also be a fishproduct, or pet companion food, a livestock or an aquaculture feed. Thefoodstuff can also be bread, tortillas, cereal, sausage, chicken, icecream, yogurt, milk, salad dressing, rice bran, fruit juice, a drybeverage powder, rolls, cookies, crackers, fruit pies, or cakes.

Also disclosed is a method of lowering cholesterol levels, triglyceridelevels, or a combination thereof in a subject, comprising the step ofadministering an effective amount of a composition comprising aeukaryotic microorganism having an 18S sequence, wherein the 18Ssequence has at least 94% identity to the sequence set forth in SEQ IDNO:1, a nutritional supplement comprising a composition comprising aeukaryotic microorganism having an 18S sequence, wherein the 18Ssequence has at least 94% identity to the sequence set forth in SEQ IDNO:1, a delivery device comprising a composition comprising a eukaryoticmicroorganism having an 18S sequence, wherein the 18S sequence has atleast 94% identity to the sequence set forth in SEQ ID NO:1, or afoodstuff comprising a composition comprising a eukaryotic microorganismhaving an 18S sequence, wherein the 18S sequence has at least 94%identity to the sequence set forth in SEQ ID NO:1.

Also disclosed is a method of supplementing essential trace elements ina subject, the method comprising the step of administering an effectiveamount of a composition comprising a eukaryotic microorganism having an18S sequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a method improving insulin sensitivity in a subject,comprising the step of administering an effective amount of acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a method of reducing hyperglycemia in a subject,comprising the step of administering an effective amount of acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a method of reducing hypercholesterolemia in asubject, comprising the step of administering an effective amount of acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a method of reducing body fat in a subject, comprisingthe step of administering an effective amount of a compositioncomprising a eukaryotic microorganism having an 18S sequence, whereinthe 18S sequence has at least 94% identity to the sequence set forth inSEQ ID NO:1, a nutritional supplement comprising a compositioncomprising a eukaryotic microorganism having an 18S sequence, whereinthe 18S sequence has at least 94% identity to the sequence set forth inSEQ ID NO:1, a delivery device comprising a composition comprising aeukaryotic microorganism having an 18S sequence, wherein the 18Ssequence has at least 94% identity to the sequence set forth in SEQ IDNO:1, or a foodstuff comprising a composition comprising a eukaryoticmicroorganism having an 18S sequence, wherein the 18S sequence has atleast 94% identity to the sequence set forth in SEQ ID NO:1.

Also disclosed is a method of promoting weight loss in a subject,comprising the step of administering an effective amount of acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a method of treating or preventing diabetes in asubject, comprising the step of administering an effective amount of acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a nutritional supplement comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, a delivery device comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, 10 wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1, or a foodstuff comprising acomposition comprising a eukaryotic microorganism having an 18Ssequence, wherein the 18S sequence has at least 94% identity to thesequence set forth in SEQ ID NO:1.

Also disclosed is a pharmaceutical formulation comprising a compositioncomprising a eukaryotic microorganism having an 18S sequence, whereinthe 18S sequence has at least 94% identity to the sequence set forth inSEQ ID NO:1.

VI. EXAMPLES

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how thecompounds, compositions, articles, devices and/or methods claimed hereinare made and evaluated, and are intended to be purely exemplary and arenot intended to limit the disclosure. Efforts have been made to ensureaccuracy with respect to numbers (e.g., amounts, temperature, etc.), butsome errors and deviations should be accounted for. Unless indicatedotherwise, parts are parts by weight, temperature is in ° C. or is atambient temperature, and pressure is at or near atmospheric.

1. Example 1: Isolation of ONC-T18 Thraustochytrium sp. Strain

Classical bacteriological strain purification techniques were employedin order to isolate ONC-T18 from mangrove leaves collected at AdvocateHarbor, Nova Scotia. ONC-T18 was serially cultured at 25° C. on anutrient medium agar containing 5 g L-¹ glucose, 2 g L⁻¹ peptone, 2 gL⁻¹ yeast extract and 15.0 g L⁻¹ agar to 1 L of 0.2 μm filtered seawater until purity was assured. Subsequently, a liquid medium containing15% artificial sea water (trophic marine), supplemented with a nitrogenand carbon source, being 60 g L⁻¹ glucose and 10 g L⁻¹ yeast extract,respectively, was prepared. This medium (50 ml of medium in 250 mlflasks) was inoculated with ONC-T18, then incubated at 25° C. andaerated via shaking at 120 rpm.

ONC-T18 was separated from medium via centrifugation, with cellularbiomass then washed, recentrifuged and freeze dried to completion.Cellular biomass was then weighed in order to determine cultureefficiencies with biomass per liter medium values recorded. Extractionof lipid fraction from biomass and subsequent fatty acid methyl esterseparation was performed using the Bligh & Dyer method.Transesterification was performed by transferring freeze dried cellularmaterial to a 10 ml screw-top test tube and adding 10% methanolic HCland dichloromethane to the tube, with the mixture allowed to react for 2hours at 90° C. Fatty acid methyl esters were then extracted viaaddition of hexane:chloroform, and the methyl ester component measuredvia gas chromatography (FID) in order to determine the fatty acidprofile of each microorganism and the symbiotic community (ONC-T18).Concentrations of each fatty acid methyl ester (C14:0 to C22:6) weredetermined by comparison of the GC peak areas of two internal standards(C19:0 and C23:0) added in defined amounts both at the beginning (C23:0)and end (C19:0) of the transesterification process. The total amount offatty acids per gram of dried cell biomass and the percentage content ofeach fatty acid, calculated using this method, are shown in FIG. 2.

From analysis of these results, in conjunction with those shown in FIG.1, it can be seen that ONC-T18 demonstrated the ability to produceincreased amounts of DHA, as well as marked quantities of EPA and DPA.ONC-T18, produces of approximately 25% DHA, 8.0% (n-6) DPA and 1.0% EPAwithin this non-optimized fermentation medium. Subsequently, ONC-T18 waschosen on the basis of a combination of economically desirablecharacteristics: (1) capable of maximal heterotrophic growth (comparedto control strains); (2) contain a high percentage of omega-3 highlyunsaturated fatty acids; (3) capable of growth on inexpensive nutrients;(4) thermotolerance, and are (5) euryhaline.

In addition, multiple different strains of oil producing microbes werecompared to ONC-T18. Each of these microbes is believed to comprise aThraustochyrid, and produces oil in the amounts shown in Table 3.

TABLE 3 [ ] = mg/g [ ] [ ] Total Weight DHA EPA Lipid (g) MYA-1381127.96 5.52 216.37 1.80 ATCC-20891 37.97 7.14 67.34 1.30 ONC-T01 5.187.76 50.82 0.40 ONC-T02 31.84 4.20 52.88 0.50 ONC-T03 24.87 6.97 75.000.60 ONC-T04 14.39 4.49 41.74 0.90 ONC-T05 11.37 3.97 34.89 0.10 ONC-T0627.80 6.71 63.87 0.10 ONC-T07 33.02 5.49 61.81 0.50 ONC-T08 24.48 4.8353.35 0.80 ONC-T09 63.82 4.25 109.12 0.80 ONC-T10 22.22 4.93 40.99 0.10ONC-T11 18.37 21.25 214.98 0.80 ONC-T12 57.96 9.03 96.26 0.60 ONC-T1312.90 4.57 39.52 1.30 ONC-T14 15.99 5.16 36.46 0.50 ONC-T15 15.53 5.1137.72 0.50 ONC-T16 18.02 5.55 42.12 0.50 ONC-T17 36.43 4.34 94.26 0.30ONC-T18 83.63 2.76 321.14 2.30 ONC-T19 34.71 8.07 66.14 0.60 ONC-T2019.28 6.94 66.74 0.10 ONC-T21 ONC-T22 22.72 3.26 47.58 0.60 ONC-T23ONC-T24 11.73 3.56 33.56 0.70 ONC-T25 26.99 6.11 45.67 0.60 ONC-T2614.50 6.43 39.22 0.60 ONC-T27 26.83 7.75 61.87 0.70 ONC-T28 16.62 6.0238.28 0.90 ONC-T29 14.67 4.91 34.48 0.80 ONC-T30 16.56 5.42 81.88 0.80ONC-T31 13.36 5.74 44.86 0.30 ONC-T32 19.12 6.56 53.29 0.20 ONC-T33ONC-T34 18.92 5.98 53.36 0.60 ONC-T35 ONC-T36 ONC-T37 35.69 11.06 82.730.10 ONC-T38 22.73 10.94 51.56 0.10 ONC-T39 ONC-T40 26.87 8.83 67.870.80 ONC-T41 22.85 6.65 52.63 0.50 ONC-T42 33.65 9.22 83.93 0.80 ONC-T4312.49 3.25 37.93 0.80 ONC-T44 11.71 2.93 55.05 1.10 ONC-T45 26.08 7.9570.45 0.70 ONC-T46 33.34 6.27 63.76 0.30 ONC-T47 10.01 4.77 68.02 0.70ONC-T48 26.23 3.95 69.06 0.60 ONC-T49 16.64 4.89 39.76 0.30 ONC-T5013.64 4.56 40.30 1.00 ONC-T51 ONC-T52 26.57 4.55 41.36 0.60 ONC-T5311.40 3.56 29.20 0.70 ONC-T54 10.34 3.18 29.31 0.70 ONC-T55 ONC-T56ONC-T57 ONC-T58 10.30 3.13 27.10 0.70 ONC-T59 ONC-T60 27.71 7.01 66.840.30 ONC-T61 15.72 5.62 52.56 0.40 ONC-T62 ONC-T63 20.17 8.25 62.58 0.60ONC-T64 12.16 2.97 44.73 1.10 ONC-T65 ONC-T66 ONC-T67 23.71 5.63 43.240.50 ONC-T68 22.72 6.10 41.37 0.50

It is understood that just as for ONC-T18, as described herein, a set ofoil producing microbes as represented by the oil producing capabilitiesdisclosed herein are disclosed, such as by a percentage of DHA to totaloil production, or by total DHA production, for example.

2. Example 2: Identification Eukaryotic Thraustochytrium Species ofONC-T18 Using Genetic Techniques

Using polymerase chain reaction (PCR) techniques and primers targetingthe 18S ribosomal RNA gene, being universal for all eukaryotic species,it was possible to generate PCR products of the structural genes of theeukaryotic microorganism isolated from ONC-T18 (as per example 1). PCRproducts were then sequenced and designated SEQ ID NO:1 for theeukaryotic species (see FIG. 2).

Comparison of SEQ ID NO:1 with nucleic acid sequences found in thegenomic database, GenBank (National Centre for BiotechnologyInformation, National Institute of Health, Bethesda, Md., USA) using theBLAST (Basic local alignment search tool) algorithm identified SEQ IDNO:1 as being most related to Thraustochytrium striatum [AF265338](97.5% similarity).

BLAST results for ONC-T18 Thraustochytrium sp. are shown below.

Score E Sequences producing significant alignments: (bits) Valuegi|14279326|gb|AF265338.1| Thraustochytrium striatum small subun . . .2126 0.0 gi|50508012|dbj|AB183657.1| Thraustochytriidae sp. MBIC11072gen . . . 2121 0.0 gi|54778780|gb|AY773276.1| Thraustochytriidae sp.FJN-10 18S rib . . . 1857 0.0 gi|50508019|dbj|AB183664.1|Thraustochytriidae sp. MBIC11093 gen . . . 1828 0.0gi|38524571|dbj|AB126669.1| Thraustochytrium sp. CHN-1 gene for . . .1748 0.0 gi|24817740|dbj|AB073308.2| Thraustochytriidae sp. N1-27 genefo . . . 1628 0.0 gi|50508018|dbj|AB183663.1| Thraustochytriidae sp.MBIC11092 gen . . . 1257 0.0 gi|50508017|dbj|AB183662.1|Thraustochytriidae sp. MBIC11091 gen . . . 1257 0.0gi|50508015|dbj|AB183660.1| Thraustochytriidae sp. MBIC11084 gen . . .1255 0.0 gi|50508011|dbj|AB183656.1| Thraustochytriidae sp. MBIC11070gen . . . 1255 0.0 gi|50508016|dbj|AB183661.1| Thraustochytriidae sp.MBIC11086 gen . . . 1249 0.0 gi|15823623|dbj|AB052555.1| Schizochytriumsp. KH105 gene for 18 . . . 1245 0.0 gi|50508013|dbj|AB183658.1|Thraustochytriidae sp. MBIC11075 gen . . . 1227 0.0gi|50508010|dbj|AB183655.1| Thraustochytriidae sp. MBIC11067 gen . . .1213 0.0 gi|54303872|gb|AY758384.1| Schizochytrium sp. FJU-512 18Sriboso . . . 1158 0.0 gi|14279326|gb|AF265338.1|AF265338Thraustochytrium striatum sma . . . 1106 0.0gi|6492308|gb|AF155209.1|AF155209 Labyrinthulid quahog parasite . . .765 0.0 gi|16209570|gb|AY052644.1| Labyrinthulid quahog parasite QPX sma. . . 757 0.0 gi|9755031|gb|AF261664.1|AF261664 Labyrinthulid quahogparasite . . . 757 0.0 gi|58176547|gb|AY870336.1| Thraustochytriidae sp.Fng1 18S ribos . . . 735 0.0 gi|67624914|dbj|AB191425.1| Unculturedeukaryote gene for small . . . 724 0.0 gi|5509891|dbj|AB022112.1|Thraustochytrium striatum gene for 18 . . . 724 0.0gi|561884|gb|L34054.1|ULKRRE Ulkenia profunda 18S ribosomal RNA . . .702 0.0 gi|50508014|dbj|AB183659.1| Thraustochytriidae sp. MBIC11077 gen. . . 686 0.0 gi|50508008|dbj|AB183653.1| Thraustochytriidae sp.MBIC11060 gen . . . 686 0.0 gi|50508009|dbj|AB183654.1|Thraustochytriidae sp. MBIC11063 gen . . . 658 0.0gi|41391986|emb|AJ535188.1| Pleurosira cf. laevis 18S rRNA gene, . . .634 e−178 gi|28316562|gb|AF525670.1| Pleurosira laevis small subunitribos . . . 634 e−178 gi|5509889|dbj|AB022110.1| Thraustochytrium aureumgene for 18S . . . 634 e−178 gi|561883|gb|L34668.1|TUKRREThraustochytrium kinnei 18S ribosom . . . 628 e−176gi|5509894|dbj|AB022115.1| Ulkenia radiata gene for 18S rRNA 624 e−175gi|5509893|dbj|AB022114.1| Ulkenia profunda gene for 18S rRNA 624 e−175gi|5509895|dbj|AB022116.1| Ulkenia visurgensis gene for 18S rRNA 603e−169 gi|9027563|gb|AF257315.2| Thraustochytriidae sp. BS2 18S ribosom .. . 589 e−164 gi|5509886|dbj|AB022107.1| Schizochytrium limacinum genefor 18S . . . 581 e−162 gi|48727879|gb|AY620254.1| Metromonas simplexclone TC-S small s . . . 571 e−159 gi|33309650|gb|AF411282.1|Unidentified cercozoan 18S ribosomal . . . 569 e−158gi|28076844|gb|AF530543.1| Uncultured eukaryote clone AT4-68 18S . . .531 e−147 gi|30144485|gb|AY256273.1| Uncultured eukaryote isolate E170sma . . . 517 e−143 gi|30144529|gb|AY256317.1| Uncultured eukaryoteisolate D107 sma . . . 507 e−140 gi|14579477|gb|AF363207.1| Eukaryotemarine clone ME1-24 18S rib . . . 505 e−139 gi|39578677|gb|AY426906.1|Uncultured marine eukaryote clone BL0 . . . 504 e−139gi|39981869|gb|AY381216.1| Uncultured eukaryote clone BL010625.3 . . .504 e−139 gi|73533408|gb|DQ103811.1| Uncultured marine eukaryote cloneM4_ . . . 504 e−139 gi|73533402|gb|DQ103805.1| Uncultured marineeukaryote clone M3_ . . . 504 e−139 gi|73533389|gb|DQ103792.1|Uncultured marine eukaryote clone M2_ . . . 504 e−139gi|73533382|gb|DQ103785.1| Uncultured marine eukaryote clone M1_ . . .504 e−139 gi|30144534|gb|AY256322.1| Uncultured eukaryote isolate D179sma . . . 504 e−139 gi|24817738|dbj|AB073305.2| Thraustochytriidae sp.H1-14 gene fo . . . 504 e−139 gi|30268157|emb|AJ519935.1|1AST519935Aplanochytrium stocchinoi p . . . 504 e−139 gi|58531881|gb|AY882527.1|Uncultured marine eukaryote clone T41 . . . 504 e−139gi|463127|gb|L27634.1|LADDLRRNA Labyrinthuloides minuta 16S-like . . .504 e−139 gi|39981839|gb|AY381186.1| Uncultured eukaryote cloneOR000415.1 . . . 502 e−138 gi|39981824|gb|AY381171.1| Unculturedeukaryote clone HE001005.1 . . . 502 e−138 gi|18026024|gb|AY046848.1|Uncultured eukaryote isolate C3_E019 . . . 502 e−138gi|18026022|gb|AY046846.1| Uncultured eukaryote isolate C3_E017 . . .502 e−138 gi|18026014|gb|AY046838.1| Uncultured eukaryote isolateC3_E008 . . . 502 e−138 gi|18026008|gb|AY046832.1| Uncultured eukaryoteisolate C3_E002 . . . 502 e−138 gi|18025980|gb|AY046804.1| Unculturedeukaryote isolate C2_E014 . . . 502 e−138 gi|18025969|gb|AY046793.1|Uncultured eukaryote isolate C2_E002 . . . 502 e−138gi|18025801|gb|AY046625.1| Uncultured eukaryote isolate C1_E024 . . .502 e−138 gi|67624915|dbj|AB191426.1| Uncultured eukaryote gene forsmall . . . 502 e−138 gi|67624913|dbj|AB191424.1| Uncultured eukaryotegene for small . . . 502 e−138 gi|67624912|dbj|AB191423.1| Unculturedeukaryote gene for small . . . 502 e−138 gi|39981861|gb|AY381208.1|Uncultured eukaryote clone BL010320.1 . . . 500 e−138gi|14349249|dbj|AB052556.1| Thraustochytrium sp. KK17-3 gene for . . .500 e−138 gi|20218962|dbj|AB073307.1| Thraustochytriidae sp. M4-103 genef . . . 498 e−137 gi|59709960|gb|AY916582.1| Uncultured eukaryote cloneZeuk76 18S . . . 496 e−136 gi|18025960|gb|AY046784.1| Unculturedeukaryote isolate A3_E043 . . . 496 e−136 gi|18025789|gb|AY046613.1|Uncultured eukaryote isolate C1_E009 . . . 496 e−136gi|30144548|gb|AY256336.1| Uncultured eukaryote isolate D278 sma . . .496 e−136 gi|2138106|gb|U59933.1|U59933 Scybalium jamaicense 18Sribosomal . . . 496 e−136 gi|53828186|gb|AY744948.1| Phytophthorapalmivora isolate 88108 . . . 494 e−136 gi|60687349|gb|AY821976.1|Uncultured oomycete clone CV1_B2_5 sm . . . 494 e−136gi|60687347|gb|AY821974.1| Uncultured Phytophthora-like oomycete . . .494 e−136 gi|60687342|gb|AY821969.1| Uncultured oomycete clone CV1_B1_49s . . . 494 e−136 gi|39981870|gb|AY381217.1| Uncultured eukaryote cloneBL010625.3 . . . 494 e−136 gi|39981864|gb|AY381211.1| Unculturedeukaryote clone BL010320.2 . . . 494 e−136 gi|39981860|gb|AY381207.1|Uncultured eukaryote clone BL010320.6 . . . 494 e−136gi|39981844|gb|AY381191.1| Uncultured eukaryote clone BL000921.1 . . .494 e−136 gi|18026046|gb|AY046870.1| Uncultured eukaryote isolateC3_E044 . . . 494 e−136 gi|18026039|gb|AY046863.1| Uncultured eukaryoteisolate C3_E035 . . . 494 e−136 gi|18026031|gb|AY046855.1| Unculturedeukaryote isolate C3_E026 . . . 494 e−136 gi|42412527|gb|AY486144.1|Pythium insidiosum 18S ribosomal RNA . . . 494 e−136gi|73533425|gb|DQ103828.1| Uncultured marine eukaryote clone M2_ . . .494 e−136 gi|34576227|gb|AY129064.1| Uncultured marine eukaryoteUEPAC45p4 . . . 494 e−136 gi|30144522|gb|AY256310.1| Unculturedeukaryote isolate D85 smal . . . 494 e−136 gi|30144521|gb|AY256309.1|Uncultured eukaryote isolate D84 smal . . . 494 e−136gi|30144518|gb|AY256306.1| Uncultured eukaryote isolate D79 smal . . .494 e−136 gi|30144475|gb|AY256263.1| Uncultured eukaryote isolate E106sma . . . 494 e−136 gi|30144473|gb|AY256261.1| Uncultured eukaryoteisolate E94 smal . . . 494 e−136 gi|21954246|gb|AY116220.1| Unculturedeukaryote clone ANT12-26 1 . . . 494 e−136gi|41393027|emb|AJ535176.1|LMI535176 Leptocylindrus minimum 18S . . .494 e−136 gi|53693111|gb|AY742743.1| Phytophthora tropicalis isolate129F- . . . 494 e−136 gi|53693108|gb|AY742759.1| Pythium vexans isolatePyv6-2 18S rib . . . 494 e−136 gi|53693105|gb|AY742756.1| Pythiumsplendens isolate 117 18S rib . . . 494 e−136 gi|53693104|gb|AY742755.1|Pythium aphanidermatum 18S ribosomal . . . 494 e−136gi|53693097|gb|AY742748.1| Phytophthora capsici isolate 98110 18 . . .494 e−136 gi|53693096|gb|AY742747.1| Phytophthora tropicalis isolate23047 . . . 494 e−136 gi|53693094|gb|AY742745.1| Phytophthora palmivoraisolate 8829 1 . . . 494 e−136 gi|58531862|gb|AY882508.1| Unculturedmarine eukaryote clone T53 . . . 494 e−136

3. Example 3: Optimized Production of Biomass Using Strain ONC-T18

Production of microbial derived (or single celled) oils are dependent ona variety of process variables, such as initial inoculum level, type ofsubstrate, media composition, temperature and pH. Specifically,microbial-based production of highly unsaturated fatty acids usingThraustochytrid strains, shows a direct correlation between biomass andfatty acid production. Consequently, an understanding of the basic needsor optimization of parameters is an important factor in achievingmaximum output. Therefore, in order to determine the best medium forproduction of increased fatty acid quantities, initial biomassoptimization experiments were undertaken. Specifically, the recentlydeveloped Taguchi method (Joseph J and Piganatiells J R, IIE Trans20:247-254, 1998), based on orthogonal arrays, was used in order todetermine the optimum medium configuration for increased optical density(directly related to biomass production). In this instance, the Taguchimethod was used to gain an understanding of the cumulative effects ofthe variables that pose an impact on biomass production. The effects ofvariations in nitrogen (yeast extract, peptone, L-glutamate), carbon(glucose) and salt 10 concentration (artificial sea salt) had on biomassproduction. Therefore, a variety of liquid media were prepared withvarying amounts of yeast extract, peptone and L-glutamate (0, 4, 10, 20,50 g L⁻¹) as relates to varying amounts of glucose and sea salt solution(5, 40, 100, 160, 200 g L⁻¹ and 0, 6, 20, 30, 40 g L⁻¹, respectively).Concentrations were calculated according to a L25 orthogonal array insuch a way that nitrogen medium of choice was discerned through the useof signal to noise ratio (SNL) analysis at 48 and 120 hrs, using thefollowing formula:

${SNL} = {{- 10}\mspace{14mu}{\log\left\lbrack {\frac{1}{n}{\sum\limits_{i = 1}^{n}\frac{1}{y_{i}^{2}}}} \right\rbrack}}$where, n=number of levels and y=yield (average OD₆₀₀ from triplicateexperiments).

Results from these experiments (which specifically target biomassconsiderations), as shown within FIG. 2 below, demonstrated that therate of nitrogen utilization by ONC-T18 as relates to optical density(OD₆₀₀) was peptone, then yeast extract followed by L-glutamate.However, based on growth maxima the best nitrogen sources for increasebiomass production was yeast extract, then peptone, followed byL-glutamate. Furthermore, through the use of similar experiments withvariations in glucose and salinity (sea salt concentration), the optimaland cheapest medium composition for the production of ONC-T18 biomasswas within a medium comprising 2 g L⁻¹ yeast extract, 8 g L⁻¹ MSG, 60 gL⁻¹ glucose and 6 g L⁻¹ sea salt.

4. Example 4: Optimized Production of Docosahexaenoic Acid (DHA) byStrain ONC-T18

Media consisting of a nitrogen source (either peptone, yeast extract,L-glutamate (MSG) or combinations of these) and a carbon source(glucose), in a saline (artificial sea water) solution, were prepared inorder to determine the best media composition for optimal biomass andDHA production in a similar manner to that described in Example 3 (shownin Table 4). After cultivation at 25° C. and 130 rpms over 3 days,biomass, total fatty acid per liter of medium, percent content of fattyacids by weight, percent content of DHA in total fatty acids and theamount of DHA per liter of medium were determined via gas chromatographyas per method described in example 1, and herein, and shown in Table 4below.

In this case, DHA was confirmed by comparison to known standards of DHAusing gas chromatography mass spectrometry and peak locking methods.Findings from experimental package

, where variations in both natural and organic forms of nitrogen wereinvestigated, showed that the optimal media composition should containbetween 4.0 and 6.0 g L⁻¹ of both yeast extract and L-glutamate foroptimal biomass and DHA production. Experimental package

, on the other hand, which investigated changes in the composition ofsodium added to the medium showed optimal DHA production and biomassproduction when artificial sea salt is used. Moreover, experimentalpackage

, in which the concentration of sodium within the medium was varied,depicted maxima for DHA and biomass production between 5 and 15%artificial seawater L⁻¹ dH₂O. Results from experimental package

, where variations in glucose levels were evaluated, demonstrated thatthe range of 40 to less than 160 g L⁻¹ glucose translated into optimalbiomass and DHA production. Finally, results of experimental package

indicate that ONC-T18 produced equivalent values for both cellularbiomass and DHA concentration, when glucose or glycerol were used ascarbon sources.

TABLE 4 Results of DHA production optimization experiments with respectto variations in medium compositions. Salt types Carbon Sources AmountNitrogen Sources Total Percent Percent Carbon Amount added Yeast fattyfatty content Amount Exp source added Salt mix (% extract MSG acidsacids DHA of DHA No. used (g L⁻¹) used salinity (g L⁻¹) (g L⁻¹) (g L⁻¹)(wt %) (wt %) (g L⁻¹)  

  401 Glucose 60.0 Sea salt 15.0 10.0 0.0 7.7 34.53 20.20 1.5579 402Glucose 60.0 Sea salt 15.0 8.0 2.0 10.0 44.01 17.09 1.7156 403 Glucose60.0 Sea salt 15.0 6.0 4.0 11.5 50.69 16.23 1.8624 404 Glucose 60.0 Seasalt 15.0 4.0 6.0 16.9 69.07 24.19 4.0877 405 Glucose 60.0 Sea salt 15.02.0 8.0 21.3 81.73 20.99 4.4752 406 Glucose 60.0 Sea salt 15.0 0.0 10.00.15 1.97 28.81 0.0426  

  407 Glucose 60.0 Sea salt 15.0 10.0 0.0 13.2 58.92 31.44 4.1362 408Glucose 60.0 NaCl 15.0 10.0 0.0 9.6 63.75 38.45 3.7009 409 Glucose 60.0NaSO₄ 15.0 10.0 0.0 0.05 1.41 20.14 0.0109  

  410 Glucose 60.0 Sea salt 5.0 10.0 0.0 14.6 59.23 31.44 4.6004 411Glucose 60.0 Sea salt 15.0 10.0 0.0 10.8 51.01 26.17 2.8144 412 Glucose60.0 Sea salt 37.5 10.0 0.0 15.9 69.32 25.32 4.0194 413 Glucose 60.0 Seasalt 75.0 10.0 0.0 10.8 61.02 25.25 2.7356 414 Glucose 60.0 Sea salt100.0 10.0 0.0 11.8 68.21 24.02 2.8290 415 Glucose 60.0 Sea salt 125.010.0 0.0 11.2 59.63 22.56 2.5256  

  416 Glucose 5.0 Sea salt 15.0 10.0 0.0 0.63 5.21 29.18 0.1844 417Glucose 20.0 Sea salt 15.0 10.0 0.0 4.06 29.59 24.01 0.9752 418 Glucose40.0 Sea salt 15.0 10.0 0.0 9.91 59.39 23.88 2.3665 419 Glucose 60.0 Seasalt 15.0 10.0 0.0 10.76 51.01 26.17 2.8144 420 Glucose 100.0 Sea salt15.0 10.0 0.0 12.79 69.50 31.55 4.0344 421 Glucose 160.0 Sea salt 15.010.0 0.0 1.00 9.40 30.01 0.3013  

  422 Glucose 5.0 Sea salt 15.0 10.0 0.0 0.62 12.74 29.86 0.1866 423Glycerol 5.0 Sea salt 15.0 10.0 0.0 0.52 18.84 35.07 0.1836

5. Example 5: Optimal Time for Harvesting of ONC-T18 for Maximal DHAProduction

ONC-T18 was cultured under the same media composition and conditions asthose shown within example 1. Of interest in this particular instance isthe time at which ONC-T18 should be harvested in order to gain themaximal amounts of DHA, DPA and EPA as well as taking into account thetime necessary to gain said amounts (see FIG. 3).

Time course experimental results showed that the optimal time forharvesting ONC-T18 for optimal DHA production within flask andbioreactor varied between 3 and 5 days, respectively.

6. Example 6: Analysis of Lipids Derived from ONC-T18

The total lipid fraction of ONC-T18 was extracted using a modified Bligh& Dyer method. Specifically, 2.0 g of dried cell biomass was rehydratedovernight at 4° C. in 8 ml of distilled H₂O. 30 ml ofmethanol:chloroform (2:1 vol/vol) was added to mixture and gently shakenat 120 rpm for 20 min, with resultant supernatant decanted. Pellet wasthen resuspended in methanol:chloroform:H₂O (2:1:0.8 vol/vol/vol) andthe process repeated with supernatants being pooled and moved to aseparation funnel. 5 ml of chloroform and 5 ml of H₂O were then added tofunnel resulting in the formation of a two-phase liquid system. Aftervigorous mixing within separation funnel, the chloroform layer wasremoved, concentrated under N₂ gas, resuspended in chloroform and storedat −20° C. under analyzed. Approximately 1 μl of the total lipidfraction was spotted on multiple chromarods, separated and analyzedusing an Iatroscan MK6 TLC/FID instrument.

Analysis of results shows that the fatty acid component which ONC-T18produces under heterotrophic fermentation is almost entirelytriglyceride (at least 95%) in nature. In addition to the neutral fattyacid fraction mentioned above. ONC-T18 also produces a discernablecarotenoid and phospholipid fraction. On subsequent isolation of thephospholipid fraction, first via a 50% and then a 75% burn followed bysolvent-based separation, it was determined that a large and complexphospholipid fraction was present. Results showed the present ofphosphotidylcholine, phosphotidylserine and phosphotidic acid componentswithin the sample.

7. Example 7: Production of Antioxidants Using the Strain, ONC-T18

The eukaryote, ONC-T18 was cultured using conditions and medium asmentioned previously. The resultant cellular biomass after heterotrophicfermentation is collected via centrifugation, filtration or settling.Cells were harvested by centrifugation at 3800×g and washed withphosphate buffered saline. The cellular biomass (fresh or freeze-dried)was suspended in 10× volume of acetone, agitated for 5 minutes at 200rpm, centrifuged at 3800×g for 5 minutes and concentrated to dryness byN₂ evaporation. The pigments were then immediately resuspended in aminimal amount of 10% acetone in hexane and stored at −20° C. until HPLCanalysis. Identification of carotenoid extracts was then carried out onan Agilent 1100 HPLC (Agilent, Palo Alto, Calif., USA) equipped with avariable wavelength detector set at 470 nm. Samples were injectedthrough a Symmetry C18 guard column (Waters, Milford, Mass., USA) to aBondclone C18 reverse-phase column (Phenomenex, Torrance, Calif., USA;10 μm particles; 3.9×300 mm i.d.). The injection volume was 10 μl and aflow of 1.00 ml/min 10% acetone in hexane over a 25 minute period wasused. Quantitative data of carotenoids was based on comparison of thepeak area with known standards (in this case astaxanthin, canthaxanthin,β-cryptoxanthin, zeaxanthin, echinenone and β-carotene; ChromaDex, SantaAna, Calif., USA). In the absence of a known standard such as in thecase of the carotenoid, phoenicoxanthin, the astaxanthin peak area wasused to calculate its concentrations. Carotenoid identity was furtherconfirmed via HPLC-MS using a Waters HPLC equipped with a photo-diodearray (Waters model 996) leading into a Micromass ESI-Q-T of Massspectrometer (Waters, Milford, Mass., USA). HPLC analysis of ONC-T18subsequently revealed the presence of several antioxidant compounds(between 50 to 1250 mg kg⁻¹) within the cellular biomass. Thesecompounds included the antioxidant carotenoids astaxanthin, zeaxanthin,canthaxanthin, echineone and beta-carotene in the range of 1 to 20 mgkg⁻¹, 0.25 to 10 mg kg⁻¹, 1 to 20 mg kg⁻¹ 1 to 20 mg kg⁻¹ and 1 to 200mg kg⁻¹, respectively, as well as several unidentified flavenoidpolyphenolic compounds.

8. Example 8: Comparison with Known Microorganisms

The ability of ONC-T18 to produce DHA, EPA and DPA was compared withthat of known microorganisms. The amount of cellular biomass per literof medium, the percent 25 content of fats or fatty acids per dried cellbiomass, the percent content of DHA, EPA and DPA in total fatty acids,and the amount of DHA, EPA and DPA obtained when DHA, EPA and DPA areproduced by cultivation of Thraustochytrium aureum ATCC 34304,Thraustochytrium sp. ATCC 20891, Thraustochytrium sp. ATCC 20892,Thraustochytrium roseum ATCC 28210, Thraustochytrium sp. ATCC 26185,Schizochytrium sp. ATCC 20888, Schizochytrium aggregatum ATCC 28209 andSchizochytrium limacinum MYA-1381, as well as when DHA, EPA and DPA areproduced by cultivation of ONC-T18 according to the present invention.

TABLE 5 Comparison of the lipid production and biomass characteristicsof several representative Thraustochytrid strains. Cellular PercentPercent Percent Percent biomass lipid content content content TotalTotal Total amount content of DHA of EPA of DPA DHA EPA DPAMicroorganism (gl⁻¹) (% g⁻¹) (% g⁻¹) (% g⁻¹) (% g⁻¹) (gl⁻¹) (mg 1⁻¹) (mg1-1) Thraustochytrium sp ATCC 20891 1.8 no data 12 no data no data nodata no data no data Thraustochytrium sp ATCC 20892 3 7 35 no data nodata 0.07 no data no data Thraustochytrium sp ATCC 26185 2.3 no data41.9 3.1 10 no data no data no data T. aureum ATCC 34304 4-5  8-20 24-513.6-9.3 no data 0.1-0.5 0.0001 no data T. roseum ATCC 28210  8-17 18-2550 no data no data 0.6-2.1 no data no data Schizochytrium sp. ATCC 2088810.5 50 25-37 no data no data 1.95 no data no data S. aggregatum ATCC28209 1.4 1.7 6.0 6.1 no data 1 1 no data S. limacinum SR21 MYA-138123-40   40-53.5 29.7-34   0.2-0.4 no data 3.0-7.2 0.08 no data ONC-T1825-55 45-80   24-34.2 0.1-2   6-10 4.6-13  0.2-0.8 0.9-3.8

As shown in Table 5, it is apparent that, when cultivation is carriedout using ONC T18 according to the present invention, the cellularbiomass values per liter medium were extremely high as compared with theother strains tested. Moreover, according to the present invention,ONC-T18 has a very high percent content of lipids compared with theother strains mentioned above. Furthermore, according to the presentinvention, the percent content of DHA and DPA within ONC-T18 isextremely high, with EPA levels shown to be comparable to all strainsscreened. Thus, it appears that ONC-T18 has the ability to produce largequantities of DHA, EPA and DPA under fermentation conditions asmentioned within example 1.

9. Example 9: Alternative Carbon Source Information

ONC-T18 has been shown to grow preferentially on media where the mainnitrogen sources are yeast extract, sodium glutamate and/or peptone andthe main carbon source is D-glucose. As a result of detailed metabolicprofiling of ONC-T18 it was noted that glycerol (carbon source) was alsoa viable alternative. Furthermore, fish oil processing waste streamscontaining glycerol were also tested for applicability as low-costnutrient alternatives. Experiments using 200 ml media in 500 ml flasks,grown at 25° C. for 3 days, 120 rpm in the case of the glycerol wereundertaken. The glycerol content of two fish oil processing wasteproducts, GWW (glycerol water wash) and GAW (glycerol acid wash),constituted 40% vol:vol of the 200 ml medium (adjusted to pH 6.5), while6% glycerol was added to 200 ml medium (wt:vol) as control.

TABLE 6 Fatty acid, biomass and glycerol content for alternative carbonsource study. Percentage (%) fatty add to total lipid content by weightTFA Glycerol Biomass AA EPA DHA DPA n-3 DPA n-6 (mg g⁻¹) (g L⁻¹) (g L⁻¹)6% Glycerol (wt:vol) 0.29 0.52 26.31 0.24 9.49 426.12 76.00 9.13 40% GAW(vol:vol) 0.37 1.32 19.69 0.42 6.36 294.55 68.59 5.94 40% GWW (vol:vol)0.46 5.55 12.46 1.01 3.82 274.33 2.70 3.08

Analysis of these results has determined that the use of fish oil wastestream components, such as glycerol by-products, as carbon sources inlarge-scale fermentation of ONC-T18 while resulting in a reduced totalfatty acid amount, represent a maintained DHA content within themicrobial cells (FIG. 10).

10. Example 10: Multiplier of Dry Cell Weight

Thraustochytrium sp. ONC-T18 can be grown for the production of omega-3oils in a variety of reactor configurations up to 100,000 L. Allfermentations begin with the preparation of a 10-20% final volumeinoculum, which is used to establish the fermentation culture. Initialmedium configurations comprise up to 6 g/L sea salt, 10 g/L nitrogensource and 60 g/L carbon source, with fed-batch addition of another 75g/L carbon source after 24 to 36 hours of initial fermentation for anadditional 72 to 96 hours and occurs within the temperature range 18-25°C. For example, using the medium 6 g/L sea salt, 2 g/L yeast extract, 8g/L L-glutamate and 60 g/L D-glucose (with an addition 75 g/L addedafter 36 hours), grown at 25° C. for 96 hours, ONC-T18 was able toproduce 40 g/L dry cell weight (dcw), 80% (dcw) total fatty acid(TFA)/lipid fraction (between C14:0 and C24:0) and 30% (TFA) DHA.Similarly, it is possible to increase dry cell weight by multiplyingboth nitrogen and carbon media components to exact a similarmultiplication effect on biomass without affecting either TFA or DHAcontents. For example, using the medium 24 g/L sea salt, 8 g/L yeastextract, 32 g/L L-glutamate and 300 g/L D-glucose, grown at 25° C. for312 hours, ONC-T18 was able to produce 80 g/L dry cell weight (dcw), 60%(dcw) total fatty acid (TFA)/lipid fraction (between C14:0 and C24:0)and 38% (TFA) DHA.

11. Example 11: Growth of Thraustochytrium Sp. ONC-T18 on VariousAlternative, Carbon (C) and Nitrogen (N) Sources and the Effect on DryCell Weight and Lipids

Growth of Thraustochytrium sp. ONC-T18 on a variety of low-cost nitrogenand carbon sources was investigated. Specifically, 50 ml of ONC-T18 wascultured in 250 ml flasks containing 6 g/L artificial sea salts, for 72hours at 25° C. Carbon and nitrogen source concentrations are shownbelow with 2 g/L of each nitrogen source listed, used in conjunctionwith 8 g/L of L-glutamate (with the exception of fish meal where 4 g wasused). Carbon sources were switched as indicated. All experiments wereperformed in triplicate; all extractions for fatty acid methyl esteranalysis were performed in triplicate along with triplicate GCinjections.

Results indicate that Thraustochytrium sp. ONC-T18 produces optimal drycell biomass (i.e. greater than the two control media) when grown on thenitrogen sources EMD yeast extract and fish meal. Conversely, lipid wasfound to be less than control, while DHA was optimal using corn steepliquor and EMD peptone. Finally, the carbon source dextrose was found toincrease lipid content, while fructose and dextrose producing high DHAcontent than the controls.

TABLE 7 Growth of Thraustochytrium sp. ONC-T18 Medium (salt 6 g/l,growth72 hrs, 50 ml dcw/l Lipid Lipid DHA DHA DHA cultures) C (g/l) N (g/l)medium (g) (mg/g) (g/l) (mg/g) (g/l) (% lipid) Nitrogen Corn SteepLiquor-MSG 60 10 11.36 371.97 4.33 111.64 1.244 29.72 Sources CottonSeed-MSG 60 10 9.99 297.08 2.70 45.20 0.500 16.94 EMD ™ YE-MSG 60 1015.49 343.90 5.02 70.68 0.786 20.70 EMD ™ YE 60 10 35.79 189.01 6.7637.14 0.448 19.65 EMD ™ Peptone-MSG 60 10 11.70 379.48 4.19 83.50 0.92623.33 Sigma ™ YE-MSG 60 10 9.77 257.86 3.28 54.60 0.618 19.69 Sigma ™ YE60 10 10.39 341.98 3.53 58.30 0.629 17.01 Fermtech ™ YE-MSG 60 10 13.99269.53 3.82 56.97 0.664 21.10 Fermtech ™ YE 60 10 17.07 243.23 4.1548.01 0.530 19.74 Fish meal (62% protein) 60 12 19.53 290.72 5.68 73.590.828 25.31 Carbon Fructose 60 10 14.57 498.54 8.09 96.97 1.070 21.55Sources Dextrose 60 10 14.98 623.91 9.87 113.69 1.232 18.94 Corn Dextrin60 10 4.65 89.69 0.39 25.69 0.278 26.75 Gelatin 60 10 7.09 31.87 0.1311.86 0.127 27.70 Starch (corn) 5 10 4.85 94.04 0.46 19.49 0.206 20.7230 10 3.13 90.07 0.28 23.78 0.256 26.40 Starch (wheat) 5 10 8.03 86.960.47 17.62 0.185 17.76 30 10 18.16 18.59 0.34 3.83 0.042 20.58 Controlmedium (1) 60 10 16.92 487.59 8.25 70.87 0.768 13.25 Control medium (2)60 10 10.88 483.06 6.06 74.64 0.818 16.19 Abbreviations: MSG =L-glutamate (sodium) YE = Yeast extract

12. Example 12: Extraction Techniques for Isolation of Total Lipids andFractions

A variety of methods for the isolation of selected omega-3 oils weretested in order to determine optimal isolation efficiency. These methodsincluded: the standard Bligh & Dyer method (Bligh & Dyer, Can J.Biochem. Physiol., 37:912-917, 1959); the combined extraction andtransesterification method used specifically with Thraustochytridspecies allowing for processing of samples for rapid GC FAME analysis(Lewis et al., J. Microbiol. Methods, 43:107-116, 2000); extraction bysimultaneous saponification (Cartens et al., J. Am. Oil Chem. Soc.73:1025-1031, 1996); and solid phase extraction using silica gel columnswhich can selectively isolate triglycerides, diglycerides andmonoglycerides (Pinkart et al., J. Microbiol. Methods, 34:9-15, 1998;Bateman & Jenkins, J. Agric. Food Chem., 45:132-135, 1997).

Specifically, 40 grams of dry cell weight Thraustochytrium sp. ONC-T18biomass produced in a single fermentation run (see example 1) wasdivided into 0.44 g lots and used for each technique. All techniqueswere performed in triplicate with efficiencies analyzed using fatty acidmethyl ester determination via FID-GC, again in triplicate withtriplicate runs per sample. Results demonstrate that total fatty acidcontent might vary between individual methods with fluctuations mostprobably due to solvent:compound saturation, biomass disruptionconsiderations and other physical condition considerations (e.g.temperature and time).

TABLE 8 Extraction Techniques for isolation of total lipids andfractions. Bligh and Dyer DHA EPA C14:0 C14:1 C15:0 C16:0 C16:1 C18:1C20:0 C20:4 C22:5 TFA mg omega-3 per gram of biomass (mg/g) 1 104.394.25 36.28 5.82 113.94 77.27 4.92 44.01 1.13 1.67 28.86 430.99 2 136.755.45 46.51 7.40 142.96 98.38 6.07 56.49 1 .40 2.19 37.92 552.98 3 134.594.78 42.51 6.91 128.54 87.01 5.20 51.10 1.30 2.10 35.98 532.91 Av.125.24 4.83 41.77 6.71 128.48 87.55 5.40 50.53 1.28 1.99 34.25 505.63Direct Transesterification DHA EPA C14:0 C15:0 C16:0 C16:1 C18:0 C18:1C20:0 C20:4 C22:5 TFA mg omega-3 per gram of biomass (mg/g) 1 104.394.24 36.39 5.42 112.94 75.27 5.42 44.01 1.13 1.67 28.86 420.99 2 89.834.54 34.81 5.60 103.04 73.43 5.56 42.85 0.98 1.87 25.35 392.88 3 101.644.25 37.16 5.98 106.94 75.98 5.35 43.95 1.11 1.78 26.46 410.65 Av. 98.654.34 36.12 5.67 107.64 74.89 5.44 43.60 1.07 1.77 26.89 408.17Simultaneous saponification DHA EPA C14:0 C15:0 C16:0 C16:1 C18:0 C18:1C20:0 C20:4 C22:5 TFA mg omega-3 per gram of biomass (mg/g) 1 204.856.75 46.55 8.56 182.26 134.81 8.73 105.04 2.16 3.20 66.68 785.25 2188.51 6.17 47.64 9.32 208.29 121.25 10.35 95.80 2.53 2.89 61.41 770.143 198.25 6.12 47.21 9.65 207.71 136.51 9.58 98.50 2.41 3.10 63.58 782.54Av. 197.20 6.35 47.13 9.18 199.42 130.86 9.55 99.78 2.37 3.06 63.89779.31 Solid phase extraction DHA EPA C14:0 C15:0 C16:0 C16:1 C18:0C18:1 C20:0 C20:4 C22:5 TFA mg omega-3 per gram of biomass (mg/g) 1169.17 0.42 68.41 10.83 204.43 140.14 8.09 76.97 1.75 3.00 47.05 748.332 172.26 0.44 69.59 11.01 207.01 143.74 8.11 78.72 1.74 3.27 47.86819.04 3 171.65 0.43 69.21 11.31 208.97 146.64 8.16 77.64 1.73 3.6446.98 785.64 Av. 171.69 0.43 69.07 11.05 206.80 143.51 8.12 77.78 1.743.30 47.30 784.34 N.B: Each value listed above is the average oftriplicate runs using FID-GC for FAME analysis

13. Example 13

a) Materials and Methods

(1) Isolation and Maintenance of Thraustochytrids

Seventy marine samples including: Spartina alterniflora, Zostera marinaand sediment were collected in eastern Canadian coastal sites from NovaScotia, Prince Edward Island, New Brunswick, Newfoundland and Labradorbetween July and August 2002. Samples were placed in 20 mL vialscontaining 10 mL of sterile 0.2 μm filtered natural seawater and 300 mgL⁻¹ penicillin and 500 mg L-¹ streptomycin. Suspensions were baited withsterile pollen (Acer sp.) and incubated for 48 hours at 18° C.,according to (Bremer, Marine Mycology—A Practical Approach, FungalDiversity Press, Hong Kong, pp 49-61 (2000)). Pollen grains were thentransferred by loop and streaked onto B1 agar plates (1 g L⁻¹ yeastextract, 1 g L⁻¹ peptone, 10 g L⁻¹ agar to 1 L natural seawater)containing antibiotics and incubated. Single, irregular, hyalinecolonies made up of spherical or limaciform cells and atypical of eitheryeast or bacterial colonies were picked and sub-cultured at least threetimes on B1 plates for purity.

(2) Biomass Production for Fatty Acid Screening

To screen isolates for growth and fatty acid production, liquid mediumwas prepared using 0.2 μm filtered natural seawater containing 2 g L⁻¹peptone (BD, Franklin Lakes, N.J., USA) and 2 g L⁻¹ yeast extract (BD,Franklin Lanes, N.J., USA), which was sterilized by autoclaving,followed by the addition of 5 g L⁻¹, 0.2 μm filter sterilized glucose(Sigma-Aldrich, St. Louis, Mo., USA) (Bowles et al., J Biotechnol70:193-202 (1999)). A 30 mL volume culture was inoculated by loop froman agar plate and grown for 4 days at 18° C. on a shaker at 100 RPM. 5mL of this culture was then used to inoculate a 95 ml culture incubatedfor a further 4 days (stationary phase). Cells were harvested bycentrifugation at 4,500 RPM, rinsed with 5 mL of distilled water andre-centrifuged. The cell pellets were freeze dried, weighed and storedat −80° C. prior to derivatisation for fatty acid analysis.

(3) Preparation of Fatty Acid Methyl Esters (FAME)

Fatty acid methyl ester (FAME) extraction was via the directtransesterification method, modified from Lewis et al. (J MicrobiolMeth. 43:107-116 (2000)). Specifically, 20 mg of freeze dried materialand 3 ml of transesterification reaction mix (methanol:hydrochloricacid:chloroform (10:1:1 vol/vol)) were added. Cells were vortexed for 10seconds to ensure even dispersal of biomass and placed at 90° C. for 120minutes. Once transesterification was complete, samples were removed andallowed to cool to room temperature. Water (1 ml) was then added andvortexed for 10 seconds. FAMEs were then extracted via the addition of3×2 ml aliquots of hexane:chloroform (4:1), vortexed for 10 seconds andallowed to sit until clear liquid separations were achieved.

(4) Gas Chromatographic (GC) Analysis of FAMEs

GC analysis of FAMES was carried out using two internal standards (200μl each). One hexacosaenoic acid (C23:0) is added prior totransesterification and the other, nonadecaenoic acid (C19:0) addeddirectly before analysis. Analyses was performed using an Agilent 6890GC (Agilent Technologies, Palo Alto, Calif., USA) equipped with a 30m×0.32 m internal diameter (0.25 μm film thickness) OMEGAWAX 320fused-silica capillary column (Sigma-Aldrich, St. Louis, Mo., USA) andflame ionization detector (injection volume 1 μl, carrier gas H2 with aconstant flow of 5.0 ml min-1 and set at 250° C., split ratio 50:1 toFID detector at 275° C.). Confirmation of FAME identity was performedusing a Trace GC-DSQ mass spectrometer (Thermo Electron, Boston, Mass.,USA) and comparison of retention times for laboratory standards.

(5) Genetic Identification

The genomic DNA was extracted using the MoBio UltraClean Microbial DNAIsolation Kit (MoBio Laboratories, Carlsbad, Calif., USA) according tomanufacturer instructions. The oligonucleotide primers used inamplifying the 18S rRNA gene, were modified from Honda et al. (JEukaryot Microbial. 46:637-647 (1999)) namely T185 1F5′CAACCTGGTTGATCCTGCCAGTA-3′ (SEQ ID NO:2) and T18S5R5′-TCACTACGGAAACCTTGTTACGAC-3′ (SEQ ID NO:3). A 20-μ1 PCR reactionmixture contained 2U Biolase™ DNA polymerase (Bioline, Boston, Mass.,USA), 1×NH₄ reaction buffer, 3 mM MgCl₂, 1M Betaine (Sigma-Aldrich,StLouis, Mo., USA), 200 μM of mix PCR nucleotides (Promega, Madison,Wis., USA), 1 μM of each forward and reverse primer (MWG Biotech., HighPoint, N.C., USA) and 100 ng of genomic DNA template. After an initialdenaturation step for 3 minutes at 94° C., PCR amplification wasperformed using a Eppendorf Master Cycle Gradient thermal cycler(Eppendorf, Westbury, N.Y., USA), using a program of 45 seconds at 94°C., 30 seconds at 64° C. and 2 minutes at 72° C. for 30 cycles, followedby a 10 minute final extension at 72° C. The PCR product was purifiedusing MoBio UltraClean PCR Clean-up Kit (MoBio Laboratories Inc,Carlsbad, Calif., USA) for direct sequencing (MWG Biotech., High Point,N.C., USA) using primers FA2, FA3, RA1, R (Mo et al., MarBio/140:883-889 2002), T18S1F and T18S5R. The resulting sequences werealigned and compared to nucleotide sequences of similar microorganismsstored in GenBank (Benson et al., Nucleic Acids Res 33:D34-38 (2005))using DS Gene (Accelrys, San Diego, Calif., USA). A phylogenetic treewas subsequently generated using the Neighbor-Joining method (Saito andNei, Mol Bioi Evo/4:406-425 (1987)), with the statistical significanceassessed using 1,000 bootstrap resamplings (Felsenstein, Evolution39:783-791 (1985)).

(6) Identification of Carotenoids

Cells were harvested by centrifugation at 3800×g and washed withphosphate buffered saline. Then resuspended in 10× volume of acetone(Sigma-Aldrich, St Louis, Mo., USA), agitated for 5 minutes at 200 RPM,centrifuged at 3,800×g for 5 mins and concentrated to dryness by N₂evaporation. Followed by resuspension in a minimal amount of 10% acetonein hexane prior to HPLC analysis. Identifications were carried out on anAgilent 1100 HPLC (Agilent, Palo Alto, Calif., USA) equipped with avariable wavelength detector set at 470 nm. Samples were injectedthrough a Symmetry C₁₈ guard column (Waters, Milford, Mass., USA) to aBondclone C₁₈ reverse-phase column (Phenomenex, Torrance, Calif., USA;10 μm particles; 3.9×300 mm i.d.). The injection volume was 10 μl and aflow of 1 ml min⁻¹ 10% acetone in hexane over a 25 minute period wasused. Carotenoid identity was further confirmed with mass spectrometryanalysis (Micromass ESI-QT of MS, Waters, Milford, Mass., USA).Quantitative data for each carotenoid was based on the development of acalibration curve using standards (astaxanthin, zeaxanthin,canthaxanthin, echinenone and β-carotene) and comparing peak area withdefined concentrations.

(7) Fermentation Optimization

The effect of carbon, nitrogen and sea salt on fatty acid and DHAproduction were examined using batch cultures in 250 ml Erlenmeyerflasks shaken at 130 RPM for 3 days at 25° C. Further cultivationstudies were carried out using a Biostat® Bplus Twin 5 L Bioreactor(Sartorius BBI Systems Inc., Bethlehem, Pa., USA). A 100 ml inoculum wasused to inoculate 4.9 L of medium in the bioreactor. Glucoseconcentration was measured using the Glucose (HK) Assay Kit(Sigma-Aldrich, St Louis, Mo., USA) according to the manufacturersinstructions. The media constituents and the conditions employed in thebioreactor are detailed with the relevant results.

b) Results

A collection and screening process was developed whereby members of theprotist family Labyrinthulida, especially the genus, Schizochytrium andThraustochytrium, were isolated using pollen-baiting and selectivebacteriological media. This study, covering 20 unique collection sitesdispersed throughout Atlantic Canada, produced 68 pure strains,identified microscopically. Selection of oleaginous strains, having morethan 20% of their cell dry weight being fatty acids, was based uponresults of GC PUFA profiling, biomass productivity, maximal TFA, DHA andto a lesser extent EPA concentrations (FIG. 11), according to the methodof (Lewis et al., J Microbiol Meth 43:107-116 (2000)). Values forbiomass, TFA and subsequent DHA and EPA productivities ranged from 100to 2300 mg L⁻¹, 27.1 to 321.14, 5.18 to 83.63 and 2.97 to 21.25 mg g⁻¹,respectively (FIG. 11).

All isolates which grew in liquid medium (54 out of 68), produced majoramounts of omega-3 polyunsaturated fatty acid, particularly DHA whichcomprised between 22 and 80% of the total C20 to C22 content of thesecells (FIG. 11). This confirms previous findings, wherebythraustochytrids isolated from cold temperate environments have fattyacid profiles with DHA being up to 53% of the total fatty acid present(Bowles et al., J Biotechnol 70:193-202 (1999) and Huang et al., MarBiotechnol 5:450-457 (2003)). Of particular interest is ONC-T18 whichproduces up to 90% of its C20 to C22 content as DHA which isapproximately 35% of the total intracellular fatty acids. This DHAcontent was shown to be equivalent to those of several commercialproduction strains, such as Schizochytrium sp. ATCC 20888 (32%) and S.limacinum MYA-1381/5R21 (34%) (Barclay et al, J Appl Phycol 6:123-129(1994) and Yokochi et al., Appl Microbiol Biotechnol 49:72-76, (2003)).Furthermore, all isolates synthesized eicosapentaenoic acid (EPA),varying between 2 and 20% w/w of total PUFAs identified (FIG. 11). Inaddition to the omega-3 oils produced, approximately 80% of all isolatessynthesized the omega-6 PUFAs, arachidonic acid (AA) or docosapentaenoicacids (DPA), at concentrations varying between 1 and 18% and 3 and 7%w/w, respectively (FIG. 11).

Huang et al. (Mar Biotechnol 5:450-457 (2003)) suggested that for 20thraustochytrids isolated from the tropical coastal waters of Japan andFiji, five polyunsaturated fatty acid profiles could be described,namely DHA/DPA (n-6), DHA/DPA/EPA, DHA/EPA, DHA/DPA/EPA/AA andDHA/DPA/EPA/AA/docosatetraenoic acid (Huang et al., Mar Biotechnol5:450-457 (2003)). In the case of this collection of thraustochytrids,isolated from the temperate waters of Atlantic Canada, four PUFAprofiles could be determined, three of which 25 are identical to thosementioned above, namely DHA/DPA/EPA at 7.4% of collection, DHA/EPA at13% of collection and DHA/DPA/EPA/AA, 74%, with a forth comprising amixture of DHA/EPA/AA at 5.6%.

Through direct sequencing of the 18S rDNA gene, ONC-T18 was positivelyidentified as a member of the Thraustochytrid family (GenBank AccessionNumber: DQ374149). Phylogenetic analysis indicated that ONC-T18 formed aunique group (97.5% identity) with Thraustochytrium striatum T91-6 (FIG.12) (Leander and Porter, Mycologia 93:459-464 (2001)). WhileThraustochytriidae sp. MBIC 11093, N1-27 and Thraustochytrium sp. CHN-1,collected from the coastal tropical waters of Japan, and found to besignificant producers of DHA (Carmona et al., Biosci Biotechnol Biochem67:884-888 (2003) and Huang et al., Mar Biotechnol 5:450-457 (2003)),were shown to be 96, 95.5 and 94.5% similar, respectively. Geneticdiversity is quite low between all members of the Thraustochytriidaeshown in FIG. 12, ranging from 97.5-91.0% similarity throughout. Yet,these species are globally distributed, with two-thirds isolated fromthe tropical coastal waters of Japan, China and Israel and the remainingfrom temperate waters off America, Europe and Canada.

The fatty acid profile of ONC-T18 included high contents of C22 PUFA,very low levels of C18 and C20 FA, and the occurrence of odd-chainsaturated fatty acids (15:0 and 17:0), similar to that of Schizochytriumsp. KH105 or S. limacinum SR21. Furthermore, analysis of carbon andnitrogen utilization profiles for strains ONC-T18, SR21 and KH105 showeda similar pattern of assimilation. The content of n-6 DPA in strainONC-T18 ranged from 6-10%, which seems to be extremely high whenconsidering the limited occurrence of n-6 DPA in the biosphere. Similarlevels of n-6 DPA were reported however, by Nakahara et al. (J Am OilChem Soc 73:1421-1426 (1996)) in Schizochytrium sp. SR21 (6-10%) andEllenbogen et al. (Comp Biochem Physiol 29:805-81 (1969)) in T. aureum(9.5%) and T. roseum (6.6%).

Analysis of the fatty acid profile of ONC-T18 under three differentculture configurations: (1) agar plate; (2) conical flask and (3)bioreactor and grown on the same medium (FIG. 13), shows a decrease inthe diversity of PUFAs present and an overall increase in TFA from agarplate to bioreactor. Specifically, agar plates exhibited an array ofPUFAs, while the flask and bioreactor grown cultures were dominated byone or two intermediates (FIG. 13). Compared to Thraustochytrium aureum,which grew better in flask culture than in a stirred tank fermenter(Ilda et al., J Ferment Bioeng 81:76-78 (1996)), ONC-T18 grew better ina bioreactor. This result is in agreement with that of (Nakahara et al.,J Am Oil Chem Soc 73:1421-1426 (1996)), who found that Schizochytriumsp. SR21 showed high resistance to mechanical stirring, and thereforethrived under bioreactor conditions.

Furthermore, carotenoid pigments were found to be produced in plate,flask and bioreactor fermentations of Thraustochytrium sp. ONC-T18,resulting in a pale orange discoloration. Production of theseantioxidants is maximal within bioreactor fermentations concurrentlywith fatty acid production. Moreover, through the use of HPLC massspectrometry, it was determined that these antioxidant compounds wereidentified as astaxanthin, zeaxanthin, canthaxanthin, echineone andβ-carotene (FIG. 14), being conjugated to various PUFAs. Similar resultswere reported amongst members of the thraustochytid group of protists.Specifically, Schizochytrium aggregatum was shown to produce echinenoneand canthaxanthin (Valadon, Trans Br Mycol Soc 67:1-15 (1976)), whileCarmona et al. (Biosci Biotechnol Biochem 67:884-888 (2003) and Huang etal. (Mar Biotechnol 5:450-457 (2003)) demonstrated the production ofastaxanthin, echinenone, canthaxanthin, phoenicoxanthin (not zeaxanthinas in ONC-T18) and 0-carotene by Thraustochytrium sp. CHN-1, a closerelative of ONC-T18 (FIG. 12). In this study, concentrations of thesecarotenoids were found to be an order of magnitude less than those ofCHN-1 with the major compound being β-carotene, rather than astaxanthin.Thus, within Thraustochytrium spp., PUFA and carotenoid production canbe linked so that the storage fats being produced may be protected fromoxidation.

Previously, it has been determined that the relative amounts of theprincipal fatty acid components (myristic, palmitic and oleic acids) maybe altered somewhat by changing the growth conditions of the culture(Ilda et al., J Ferment Bioeng 81:76-78 (1996)). In this way, one canmanipulate the final fatty acid composition and hence, physicalproperties of the desired PUFA in a controlled fashion duringfermentation (Sijtsma et al., Recent Res Devel Microbiol 2:219-232(1998)). In an attempt to limit the factors inhibiting both biomass andomega-3 PUFA production in ONC-T18, carbon, nitrogen and sea saltcomponents in nutrient media were manipulated (Table 9), along withduration of culture (FIG. 15).

TABLE 9 Mean biomass production (SD ≦ 15%), total fatty acid (TFA) andDHA content of Thraustochytrium SP. ONC-T18. Glucose Biomass TFA DHA DHA(g L⁻¹) (g L⁻¹) (% biomass) (% TFA) (g L⁻¹) 5 12.13 5.21 29.18 0.18 2013.73 29.59 24.01 0.98 40 16.69 59.39 23.88 2.37 60 21.08 51.01 26.172.81 100 18.40 69.49 31.55 4.03 160 10.68 9.40 30.01 0.30 YE MSG BiomassTFA DHA DHA (g L⁻¹) (g L⁻¹) (g L⁻¹) (% biomass) (% TFA) (g L⁻¹) 10 022.33 34.53 20.20 1.56 8 2 22.81 44.00 17.52 1.72 6 4 22.64 50.69 16.231.86 4 6 24.46 69.07 24.19 4.09 2 8 26.09 81.73 20.99 4.47 0 10 7.501.97 28.81 0.04 Sea salt Biomass TFA DHA DHA (g L⁻¹) (g L⁻¹) (% biomass)(% TFA) (g L⁻¹) 2 24.70 59.23 31.44 4.60 6 21.08 51.01 26.17 2.81 1522.90 69.32 25.32 4.02 30 17.76 61.02 25.25 2.74 40 17.27 68.21 24.022.83 50 18.77 59.63 22.56 2.53

Within this study, as the concentration of nitrogen decreased, totalfatty acid content increased, with the highest total fatty acid content(approximately 80%) obtained at 1% concentration of yeast extract and ormonosodium glutamate (w/v). Cultures with a low nitrogen concentration,however, also limited cell growth and hence total fatty acid production.Optimal production in this experiment was obtained using 8 g L⁻¹monosodium glutamate and 2 g L⁻¹ yeast extract, producing 26.1 g L⁻¹biomass and 4.5 g L⁻¹ DHA (Table 9). Furthermore, increases in carbon upto 100 g L⁻¹ effectively increased DHA yield, this is in agreement withresults obtained for Schizochytrium sp. SR21 (Yokochi et al., ApplMicrobiol Biotechnol 49:72-76, (2003)) and contrary to those shown in T.aureum where glucose concentrations above 10 g L⁻¹ were inhibitory (Ildaet al., J Ferment Bioeng 81:76-78 (1996)). Maximum DHA yields of morethan 4.0 g L⁻¹ were obtained in glucose medium, with yields more than 5times that of T. aureum (Bajpai et al., J Am Oil Chem Soc 68:509-514(1991)) and T. roseum (Li and Ward, J Ind Microbiol 13:238-241 (1994))and comparable to that of Schizochytrium sp. SR21 and KH105 (Aki et al.,J Am Oil Chem Soc 80:789-794 (2003)). Finally, ONC-T18 exhibitedclassical euryhaline abilities, being able to withstand salinitiesranging from 2.0 to 50.0 g L⁻¹, resulting in biomass productivity of25-30% variability (Table 9). In the same experiment DHA g L⁻¹ valueswere found to vary up to 45% between optimal at 4.6 g L⁻¹ and minimal at2.5 g L⁻¹ (Table 9).

The biomass, TFA and DHA produced by ONC-T18 over a 168 h period in a 5L bioreactor are presented in FIG. 15. The growth curve depicted istypical of several achieved under identical conditions. Maximum biomassproduction was reached after 120 h, close to the point of carbon source(i.e. glucose) depletion. This was also the point at which total fattyacid content of the biomass reached a maximum at around 70% biomass.Interestingly, after only 24 h of cultivation, DHA content spiked to 30%total fatty acid, thereafter remaining constant at 20-25%. These resultsare consistent with those of other fatty acid producing Thraustochytidstrains, yet there is disparity with regards to the rate at which thesereactions occur.

c) Discussion

Previously most studies of Labyrinturomycota identified strains whichare unable to store total fatty acid in amounts greater than 20% ofbiomass. For example, prior to the isolation of Schizochytrium sp. SR 21which is able to accumulate up to 50% of biomass as fat, T. aureum wasthe best accumulator at 20% (Bajpai et al., J Am Oil Chem Soc 68:509-514(1991)). ONC-T18, on the other hand, is able to accumulate up to 80% ofits biomass as lipid.

For oleaginous micro-organisms such as ONC-T18 to accumulate oil, ittypically should be grown in a culture medium with a limited amount ofnitrogen (usually exhausted after 24 to 36 h) and abundant amounts of acarbon source. Once the nitrogen is depleted, the oleaginous microbescontinue to assimilate the carbon source but are no longer able toundergo cell division due to a lack of nitrogen (thus preventing proteinand nucleic acid synthesis). The result being the conversion of thesecarbon sources (i.e. sugars such as glucose) into storage oils. In thisregard, ONC-T18 is considered to grow more slowly than otherThraustochytrid strains, such as G13 (Bowles et al., J Biotechnol70:193-202 (1999) and Huang et al., Mar Biotechnol 5:450-457 (2003), yetit produces DHA at faster rates and demonstrates a unique ability toincorporate elevated amounts of total fatty acids. Finally, the abilityof ONC-T18 to grow at very low salt concentrations with both highbiomass and total fatty acid productivity is remarkable. Lending itselfwell to scale up by negating the corrosive nature of salt water onindustrial fermentation equipment.

What is claimed is:
 1. A composition comprising an isolated eukaryoticmicroorganism having an 18S sequence, wherein the 18S sequence has atleast 97% identity to the sequence set forth in SEQ ID NO:1, and anartificial heterotrophic growth medium comprising a carbon source, anitrogen source, inorganic salts and vitamins, wherein the microorganismin the composition produces a lipid or fatty acid fraction of at leastabout 30 wt. % to 80 wt. %.
 2. The composition of claim 1, wherein the18S sequence has at least 99% identity to the sequence set forth in SEQID NO:1.
 3. The composition of claim 1, wherein the microorganism hasATCC Accession Number PTA-6245.
 4. The composition of claim 1, whereinthe microorganism comprises an omega 3 or omega 6 fatty acid.
 5. Thecomposition of claim 1, wherein the microorganism comprises a lipid orfatty acid fraction and wherein the lipid or fatty acid fractioncomprises docosahexaenoic acid (DHA).
 6. The composition of claim 1,wherein the microorganism is a Schizochytrium sp.
 7. The composition ofclaim 1, wherein the microorganism is a Thraustochytrium sp.
 8. Thecomposition of claim 1, wherein the medium comprises a carbon source inan amount of from 1 to 60 g L⁻¹.
 9. The composition of claim 1, whereinthe microorganism medium comprises a carbon source in an amount of from1 to 200 g L⁻¹.
 10. The composition of claim 1, wherein themicroorganism comprises neutral lipids.
 11. The composition of claim 10,wherein the microorganism comprises at least 95% by weight of totallipids.
 12. The composition of claim 1, wherein the 18S sequencecontains at least one substitution modification relative to SEQ ID NO:1.13. The composition of claim 12, wherein the 18S sequence has at least99% identity to the sequence set forth in SEQ ID NO:1.
 14. Thecomposition of claim 12, wherein the microorganism comprises an omega 3or omega 6 fatty acid.
 15. The composition of claim 12, wherein themicroorganism comprises a lipid or fatty acid fraction and wherein thelipid or fatty acid fraction comprises docosahexaenoic acid (DHA). 16.The composition of claim 12, wherein the microorganism is aSchizochytrium sp.
 17. The composition of claim 12, wherein themicroorganism is a Thraustochytrium sp.
 18. The composition of claim 12,wherein the microorganism comprises neutral lipids.
 19. The compositionof claim 18, wherein the neutral lipids comprise at least 95% by weightof total lipids.